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  • 95
    ATCC genbank
    Genbank, supplied by ATCC, used in various techniques. Bioz Stars score: 95/100, based on 557 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Biotechnology Information genbank
    A phylogenetic tree showing the relationship of BQCV isolates. The partial sequences of 3′ UTR of BQCV from A. cerana collected from different geographic locations of China and from Apis mellifera retrieved from <t>GenBank</t> were aligned using ClustalW. The sequence of IAPV was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.
    Genbank, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 94/100, based on 7654 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Bioedit Company genbank database
    Multiple alignment of Bo_GH protein sequence vs . GH protein sequence at <t>GenBank</t> goat database
    Genbank Database, supplied by Bioedit Company, used in various techniques. Bioz Stars score: 93/100, based on 492 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Unigene genbank
    ( A ) Entry for cystic fibrosis, which contains links to the CFMDB and the list of CF cell lines available for research. ( B ) An example of links from the CFTR entry to Nomenclature, RefSeq, <t>GenBank,</t> Protein and UniGene databases.
    Genbank, supplied by Unigene, used in various techniques. Bioz Stars score: 93/100, based on 598 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Thermo Fisher genbank
    ( A ) Entry for cystic fibrosis, which contains links to the CFMDB and the list of CF cell lines available for research. ( B ) An example of links from the CFTR entry to Nomenclature, RefSeq, <t>GenBank,</t> Protein and UniGene databases.
    Genbank, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 94/100, based on 2239 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Biotechnology Information genbank sequence database
    Measure of execution time (using <t>GenBank</t> database).
    Genbank Sequence Database, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 90/100, based on 434 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Biotechnology Information genbank nucleotide database
    Measure of execution time (using <t>GenBank</t> database).
    Genbank Nucleotide Database, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 89/100, based on 141 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Biotechnology Information nonredundant dna database
    Measure of execution time (using <t>GenBank</t> database).
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    92
    Sangon Biotech genbank database
    Measure of execution time (using <t>GenBank</t> database).
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    92
    Addgene inc genbank
    Measure of execution time (using <t>GenBank</t> database).
    Genbank, supplied by Addgene inc, used in various techniques. Bioz Stars score: 92/100, based on 82 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Celera genbank
    Measure of execution time (using <t>GenBank</t> database).
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    89
    Biotechnology Information japan ddbj
    Representation of SkateBase data within the The National Center for Biotechnology Information (NCBI) databases. A . The little skate genome project is represented as a BioProject entry that connects all samples and data thematically. A BioSample record describes the <t>DNA</t> sample that was used for genome sequencing that was generated from a single stage 32 skate embryo. The SRA catalogs the unassembled Illumina genome sequence data. The Whole Genome Shotgun (WGS) database contains the contiguous sequences from shotgun sequencing projects. The assembled and annotated mitochondrial genome was deposited in <t>GenBank</t> and subsequently included in the NCBI Reference Sequence Database (RefSeq). B . The project to characterize the embryonic transcriptomes of L. erinacea , C. milii and S. canicula is represented in a BioProject entry. Three BioSample entries, one for each species, lead to three SRA datasets. The transcriptome data is represented also in the Gene Expression Omnibus (GEO), a database of high-throughput functional genomic data derived from microarrays and next-generation sequencing technologies.
    Japan Ddbj, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 89/100, based on 95 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    A phylogenetic tree showing the relationship of BQCV isolates. The partial sequences of 3′ UTR of BQCV from A. cerana collected from different geographic locations of China and from Apis mellifera retrieved from GenBank were aligned using ClustalW. The sequence of IAPV was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.

    Journal: PLoS ONE

    Article Title: The Prevalence of Parasites and Pathogens in Asian Honeybees Apis cerana in China

    doi: 10.1371/journal.pone.0047955

    Figure Lengend Snippet: A phylogenetic tree showing the relationship of BQCV isolates. The partial sequences of 3′ UTR of BQCV from A. cerana collected from different geographic locations of China and from Apis mellifera retrieved from GenBank were aligned using ClustalW. The sequence of IAPV was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.

    Article Snippet: The nucleotide sequences of PCR products were determined and compared with sequences published at GenBank, National Center for Biotechnology Information, NIH.

    Techniques: Sequencing

    A phylogenetic tree showing the relationship of DWV isolates. The partial sequences of RNA dependent RNA polymerase (RdRp) of DWV from A. cerana collected from different geographic locations of China and from Apis mellifera retrieved from GenBank were aligned using ClustalW. The sequence of IAPV was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.

    Journal: PLoS ONE

    Article Title: The Prevalence of Parasites and Pathogens in Asian Honeybees Apis cerana in China

    doi: 10.1371/journal.pone.0047955

    Figure Lengend Snippet: A phylogenetic tree showing the relationship of DWV isolates. The partial sequences of RNA dependent RNA polymerase (RdRp) of DWV from A. cerana collected from different geographic locations of China and from Apis mellifera retrieved from GenBank were aligned using ClustalW. The sequence of IAPV was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.

    Article Snippet: The nucleotide sequences of PCR products were determined and compared with sequences published at GenBank, National Center for Biotechnology Information, NIH.

    Techniques: Sequencing

    A phylogenetic tree showing the relationship of C. bombi isolates. The partial sequences of 18 S ribosomal RNA of C. bombi from Apis cerana collected from different geographic locations of China and from bumble bee species retrieved from GenBank were aligned using ClustalW. The tree was built using the Neighbor-Joining method. The sequence of Trypanosoma brucei was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.

    Journal: PLoS ONE

    Article Title: The Prevalence of Parasites and Pathogens in Asian Honeybees Apis cerana in China

    doi: 10.1371/journal.pone.0047955

    Figure Lengend Snippet: A phylogenetic tree showing the relationship of C. bombi isolates. The partial sequences of 18 S ribosomal RNA of C. bombi from Apis cerana collected from different geographic locations of China and from bumble bee species retrieved from GenBank were aligned using ClustalW. The tree was built using the Neighbor-Joining method. The sequence of Trypanosoma brucei was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.

    Article Snippet: The nucleotide sequences of PCR products were determined and compared with sequences published at GenBank, National Center for Biotechnology Information, NIH.

    Techniques: Sequencing

    A phylogenetic tree showing the relationship of Nosema ceranae isolates. The partial sequences of 16S ribosomal RNA of N. ceranae from A. cerana collected in different geographic locations of China and from A. mellifera retrieved from GenBank were aligned using ClustalW. The tree was built using the Neighbor-Joining method. The sequence of Encephalitozoon cuniculi was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.

    Journal: PLoS ONE

    Article Title: The Prevalence of Parasites and Pathogens in Asian Honeybees Apis cerana in China

    doi: 10.1371/journal.pone.0047955

    Figure Lengend Snippet: A phylogenetic tree showing the relationship of Nosema ceranae isolates. The partial sequences of 16S ribosomal RNA of N. ceranae from A. cerana collected in different geographic locations of China and from A. mellifera retrieved from GenBank were aligned using ClustalW. The tree was built using the Neighbor-Joining method. The sequence of Encephalitozoon cuniculi was used as an outgroup to root the tree. Numbers at each node represent bootstrap values as percentages of 500 and only bootstrap values greater than 50% are shown.

    Article Snippet: The nucleotide sequences of PCR products were determined and compared with sequences published at GenBank, National Center for Biotechnology Information, NIH.

    Techniques: Sequencing

    Maximum-likelihood phylogenetic tree of cluster IV NifH sequences, which include divergent NifH proteins from methanogens. GenBank accession numbers in parentheses follow the isolate or clone name. Deep-sea and hydrothermal vent NifH sequences from this study are in bold, followed by the number of additional NifH sequences from this study that are ≥97% similar to it in parentheses. The letter prefix of each clone name denotes the sample from which the clone was sequenced (A, marker 33, Axial Volcano, 2000; B, deep seawater; C, diffuse vent near Puffer, Endeavour segment, 2000; and E, marker 33, Axial Volcano, 1999). Quartet puzzling support values are shown at each internal branch. The scale indicates the number of amino acid substitutions per site, and the tree is outgroup rooted with P. boryanum frxC , a dinitrogenase reductase-like protein involved in the light-independent reduction of protochlorophyllide.

    Journal: Applied and Environmental Microbiology

    Article Title: Phylogenetic Diversity of Nitrogenase (nifH) Genes in Deep-Sea and Hydrothermal Vent Environments of the Juan de Fuca Ridge

    doi: 10.1128/AEM.69.2.960-970.2003

    Figure Lengend Snippet: Maximum-likelihood phylogenetic tree of cluster IV NifH sequences, which include divergent NifH proteins from methanogens. GenBank accession numbers in parentheses follow the isolate or clone name. Deep-sea and hydrothermal vent NifH sequences from this study are in bold, followed by the number of additional NifH sequences from this study that are ≥97% similar to it in parentheses. The letter prefix of each clone name denotes the sample from which the clone was sequenced (A, marker 33, Axial Volcano, 2000; B, deep seawater; C, diffuse vent near Puffer, Endeavour segment, 2000; and E, marker 33, Axial Volcano, 1999). Quartet puzzling support values are shown at each internal branch. The scale indicates the number of amino acid substitutions per site, and the tree is outgroup rooted with P. boryanum frxC , a dinitrogenase reductase-like protein involved in the light-independent reduction of protochlorophyllide.

    Article Snippet: All 120 nifH sequences obtained in this study have been submitted to the GenBank database at the National Center for Biotechnology Information.

    Techniques: Marker

    Maximum-likelihood phylogenetic tree of cluster II NifH sequences, which include NifH from methanogens and bacterial AnfH. GenBank accession numbers in parentheses follow the isolate or clone name. Deep-sea and hydrothermal vent NifH sequences from this study are in bold, followed by the number of additional NifH sequences from this study ≥97% similar to it in parentheses. The letter prefix of each clone name denotes the sample from which the clone was sequenced (A, marker 33, Axial Volcano, 2000; B, deep seawater; C, diffuse vent near Puffer, Endeavour segment, 2000; and E, marker 33, Axial Volcano, 1999). Quartet puzzling support values are shown at each internal branch. The scale indicates the number of amino acid substitutions per site, and the tree is outgroup rooted with M. jannaschii .

    Journal: Applied and Environmental Microbiology

    Article Title: Phylogenetic Diversity of Nitrogenase (nifH) Genes in Deep-Sea and Hydrothermal Vent Environments of the Juan de Fuca Ridge

    doi: 10.1128/AEM.69.2.960-970.2003

    Figure Lengend Snippet: Maximum-likelihood phylogenetic tree of cluster II NifH sequences, which include NifH from methanogens and bacterial AnfH. GenBank accession numbers in parentheses follow the isolate or clone name. Deep-sea and hydrothermal vent NifH sequences from this study are in bold, followed by the number of additional NifH sequences from this study ≥97% similar to it in parentheses. The letter prefix of each clone name denotes the sample from which the clone was sequenced (A, marker 33, Axial Volcano, 2000; B, deep seawater; C, diffuse vent near Puffer, Endeavour segment, 2000; and E, marker 33, Axial Volcano, 1999). Quartet puzzling support values are shown at each internal branch. The scale indicates the number of amino acid substitutions per site, and the tree is outgroup rooted with M. jannaschii .

    Article Snippet: All 120 nifH sequences obtained in this study have been submitted to the GenBank database at the National Center for Biotechnology Information.

    Techniques: Marker

    Maximum-likelihood phylogenetic tree of cluster I NifH sequences, which include α-, β-, and γ-proteobacterial and cyanobacterial NifH sequences. GenBank accession numbers in parentheses follow the isolate or clone name. Hydrothermal vent NifH sequences from this study are in bold, followed by the number of additional NifH sequences from this study that are ≥97% similar to it, in parentheses. The letter prefix of each clone name denotes which sample the clone was sequenced from, as follows: A, marker 33, Axial Volcano, 2000; B, deep seawater; C, diffuse vent near Puffer, Endeavour Segment, 2000; E, marker 33, Axial Volcano, 1999. Quartet puzzling support values are shown at each internal branch. The scale indicates the number of amino acid substitutions per site, and the tree is outgroup rooted with Frankia sp.

    Journal: Applied and Environmental Microbiology

    Article Title: Phylogenetic Diversity of Nitrogenase (nifH) Genes in Deep-Sea and Hydrothermal Vent Environments of the Juan de Fuca Ridge

    doi: 10.1128/AEM.69.2.960-970.2003

    Figure Lengend Snippet: Maximum-likelihood phylogenetic tree of cluster I NifH sequences, which include α-, β-, and γ-proteobacterial and cyanobacterial NifH sequences. GenBank accession numbers in parentheses follow the isolate or clone name. Hydrothermal vent NifH sequences from this study are in bold, followed by the number of additional NifH sequences from this study that are ≥97% similar to it, in parentheses. The letter prefix of each clone name denotes which sample the clone was sequenced from, as follows: A, marker 33, Axial Volcano, 2000; B, deep seawater; C, diffuse vent near Puffer, Endeavour Segment, 2000; E, marker 33, Axial Volcano, 1999. Quartet puzzling support values are shown at each internal branch. The scale indicates the number of amino acid substitutions per site, and the tree is outgroup rooted with Frankia sp.

    Article Snippet: All 120 nifH sequences obtained in this study have been submitted to the GenBank database at the National Center for Biotechnology Information.

    Techniques: Marker

    Maximum-likelihood phylogenetic tree of cluster III NifH sequences, which include NifH sequences from diverse anaerobic bacteria like sulfate reducers and clostridia. GenBank accession numbers in parentheses follow the isolate or clone name. Hydrothermal vent NifH sequences from this study are in bold, followed by the number of additional NifH sequences from this study ≥97% similar to it in parentheses. The letter prefix of each clone name denotes the sample from which the clone was sequenced (A, marker 33, Axial Volcano, 2000; B, deep seawater; C, diffuse vent near Puffer, Endeavour Segment, 2000; and E, marker 33, Axial Volcano, 1999). Quartet puzzling support values are shown at each internal branch. The scale indicates the number of amino acid substitutions per site, and the tree is outgroup rooted with K. pneumoniae .

    Journal: Applied and Environmental Microbiology

    Article Title: Phylogenetic Diversity of Nitrogenase (nifH) Genes in Deep-Sea and Hydrothermal Vent Environments of the Juan de Fuca Ridge

    doi: 10.1128/AEM.69.2.960-970.2003

    Figure Lengend Snippet: Maximum-likelihood phylogenetic tree of cluster III NifH sequences, which include NifH sequences from diverse anaerobic bacteria like sulfate reducers and clostridia. GenBank accession numbers in parentheses follow the isolate or clone name. Hydrothermal vent NifH sequences from this study are in bold, followed by the number of additional NifH sequences from this study ≥97% similar to it in parentheses. The letter prefix of each clone name denotes the sample from which the clone was sequenced (A, marker 33, Axial Volcano, 2000; B, deep seawater; C, diffuse vent near Puffer, Endeavour Segment, 2000; and E, marker 33, Axial Volcano, 1999). Quartet puzzling support values are shown at each internal branch. The scale indicates the number of amino acid substitutions per site, and the tree is outgroup rooted with K. pneumoniae .

    Article Snippet: All 120 nifH sequences obtained in this study have been submitted to the GenBank database at the National Center for Biotechnology Information.

    Techniques: Marker

    Phylogenetic trees of plant taxa. (A) Reference tree from [ 50 ] and trees constructed with (B) the approach described here and by (C) ACS [ 21 ], (D) FFP [ 8 ], and (E) kmacs [ 22 ]. The original dataset contained 14 taxa, but only for 11 taxa could the proteomes be downloaded through GenBank. For completeness, we show the reference for all 14 taxa.

    Journal: GigaScience

    Article Title: Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences

    doi: 10.1093/gigascience/giy148

    Figure Lengend Snippet: Phylogenetic trees of plant taxa. (A) Reference tree from [ 50 ] and trees constructed with (B) the approach described here and by (C) ACS [ 21 ], (D) FFP [ 8 ], and (E) kmacs [ 22 ]. The original dataset contained 14 taxa, but only for 11 taxa could the proteomes be downloaded through GenBank. For completeness, we show the reference for all 14 taxa.

    Article Snippet: Proteins for Wolbachia strains that were lacking this information in the National Center for Biotechnology Information GenBank were derived from translations using GeneMark version 2.5 [ ].

    Techniques: Construct

    Phylogenetic trees for a large set of microbial taxa studied by Lang et al. [ 51 ]. (A) Maximum-likelihood tree constructed by Lang et al. based on a super alignment of 24 selected genes. (B) Tree constructed with our approach, as described here, for 813 taxa for which the proteomes are available in GenBank. (C) Tree constructed with our approach based on the proteins corresponding to the 24 genes selected by Lang et al. (D) Tree reconstructed using our program FSWM [ 33 ] on the 841 whole-genome sequences.

    Journal: GigaScience

    Article Title: Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences

    doi: 10.1093/gigascience/giy148

    Figure Lengend Snippet: Phylogenetic trees for a large set of microbial taxa studied by Lang et al. [ 51 ]. (A) Maximum-likelihood tree constructed by Lang et al. based on a super alignment of 24 selected genes. (B) Tree constructed with our approach, as described here, for 813 taxa for which the proteomes are available in GenBank. (C) Tree constructed with our approach based on the proteins corresponding to the 24 genes selected by Lang et al. (D) Tree reconstructed using our program FSWM [ 33 ] on the 841 whole-genome sequences.

    Article Snippet: Proteins for Wolbachia strains that were lacking this information in the National Center for Biotechnology Information GenBank were derived from translations using GeneMark version 2.5 [ ].

    Techniques: Construct

    Phylogenetic tree based on the partial amino-acid sequences of the rotavirus G6P[5] VP7 coding gene. Phylogeny was reconstructed using the maximum likelihood method implemented in the PhyML programme with the Jones Taylor Thornton substitution model. The number of substitutions per site is indicated by the scale bar. Bootstrap values were calculated for 500 replicates and are indicated at each node when ≥70%. Strains from this study which were collected in a vaccinated herd are indicated with a full circle (●), while those collected in a non-vaccinated herd are indicated with an empty circle (○). GenBank accession numbers of the reference strains used for this analysis are: RVA/Huma-wt/BEL/B1711/2002/G6P[6]: AF532202 ; RVA/Human-wt/HUN/Hun7/1998/G6P[9]: AJ488134 ; RVA/Human-wt/HUN/Hun4/1996/G6P[9]: AJ487833 ; RVA/Buffalo-tc/ITA/10733/2001/G6P[3]: AY281360 ; RVA/Human-wt/HUN/Hun5/1997/G6P[14]: EF554109 ; RVA/Human-tc/AUS/MG6/1993/G6P[14]: U22011 ; RVA/Cow-wt/USA/VMRI-29/1991/G6P[11]: U50332 ; RVA/Cow-wt/IRL/CIT-A99/XXXX/G6P[5]: GQ377868 ; RVA/Cow-wt/USA/MC27/1998/G6P[11]: AF162435 ; RVA/Cow-tc/USA/NCDV/1967/G6P[1]: M12394 ; RVA/Cow-tc/FRA/RF/1982/G6P[1]: X65940 ; RVA/Cow-tc/USA/WC3/1981/G6P[5]: AY050272 ; RVA/Cow-tc/GBR/UK/1973/G6P[5]: X00896 ; RVA/Cow-tc/USA/VMRI/XXXX/G6P[5]: U53924 ; RVA/Cow-tc/USA/B223/XXXX/G10P[11]: X57852 .

    Journal: Vaccine

    Article Title: Impact of rotavirus vaccine on rotavirus genotypes and caliciviruses circulating in French cattle

    doi: 10.1016/j.vaccine.2013.03.039

    Figure Lengend Snippet: Phylogenetic tree based on the partial amino-acid sequences of the rotavirus G6P[5] VP7 coding gene. Phylogeny was reconstructed using the maximum likelihood method implemented in the PhyML programme with the Jones Taylor Thornton substitution model. The number of substitutions per site is indicated by the scale bar. Bootstrap values were calculated for 500 replicates and are indicated at each node when ≥70%. Strains from this study which were collected in a vaccinated herd are indicated with a full circle (●), while those collected in a non-vaccinated herd are indicated with an empty circle (○). GenBank accession numbers of the reference strains used for this analysis are: RVA/Huma-wt/BEL/B1711/2002/G6P[6]: AF532202 ; RVA/Human-wt/HUN/Hun7/1998/G6P[9]: AJ488134 ; RVA/Human-wt/HUN/Hun4/1996/G6P[9]: AJ487833 ; RVA/Buffalo-tc/ITA/10733/2001/G6P[3]: AY281360 ; RVA/Human-wt/HUN/Hun5/1997/G6P[14]: EF554109 ; RVA/Human-tc/AUS/MG6/1993/G6P[14]: U22011 ; RVA/Cow-wt/USA/VMRI-29/1991/G6P[11]: U50332 ; RVA/Cow-wt/IRL/CIT-A99/XXXX/G6P[5]: GQ377868 ; RVA/Cow-wt/USA/MC27/1998/G6P[11]: AF162435 ; RVA/Cow-tc/USA/NCDV/1967/G6P[1]: M12394 ; RVA/Cow-tc/FRA/RF/1982/G6P[1]: X65940 ; RVA/Cow-tc/USA/WC3/1981/G6P[5]: AY050272 ; RVA/Cow-tc/GBR/UK/1973/G6P[5]: X00896 ; RVA/Cow-tc/USA/VMRI/XXXX/G6P[5]: U53924 ; RVA/Cow-tc/USA/B223/XXXX/G10P[11]: X57852 .

    Article Snippet: 2.4 Sequence analyses A selection of reference strains available in the National Center for Biotechnology Information GenBank database ( http://www.ncbi.nlm.nih.gov/genbank/ ) was used for all sequence analyses.

    Techniques:

    Phylogenetic tree based on the partial amino-acid sequences of the rotavirus G6P[5] VP4 coding gene. Phylogeny was reconstructed using the maximum likelihood method implemented in the PhyML programme with the Jones Taylor Thornton substitution model. The number of substitutions per site is indicated by the scale bar. Bootstrap values were calculated for 500 replicates and are indicated at each node when ≥70%. Strains from this study which were collected in a vaccinated herd are indicated with a full circle (●), while those collected in a non-vaccinated herd are indicated with an empty circle (○). GenBank accession numbers of the reference strains used for this analysis are: RVA/Cow-wt/IRL/CIT-A99/XXXX/G6P[5]: GQ414745 ; RVA/Cow-xx/THA/61A/XXXX/G10P[5]: D13396 ; RVA/Cow-tc/USA/VMRI/XXXX/G6P[5]: U53923 ; RVA/Cow-tc/USA/WC3/1981/G6P[5]: AY050271 ; RVA/Cow-tc/GBR/678/XXXX/G8P[5]: D32054 ; RVA/Cow-tc/GBR/UK/1973/G6P[5]: M22306 ; RVA/Cow-tc/USA/B641/XXXX/G6P[5]: M63267 ; RVA/Cow-tc/USA/B223/XXXX/G10P[11]: M92986 .

    Journal: Vaccine

    Article Title: Impact of rotavirus vaccine on rotavirus genotypes and caliciviruses circulating in French cattle

    doi: 10.1016/j.vaccine.2013.03.039

    Figure Lengend Snippet: Phylogenetic tree based on the partial amino-acid sequences of the rotavirus G6P[5] VP4 coding gene. Phylogeny was reconstructed using the maximum likelihood method implemented in the PhyML programme with the Jones Taylor Thornton substitution model. The number of substitutions per site is indicated by the scale bar. Bootstrap values were calculated for 500 replicates and are indicated at each node when ≥70%. Strains from this study which were collected in a vaccinated herd are indicated with a full circle (●), while those collected in a non-vaccinated herd are indicated with an empty circle (○). GenBank accession numbers of the reference strains used for this analysis are: RVA/Cow-wt/IRL/CIT-A99/XXXX/G6P[5]: GQ414745 ; RVA/Cow-xx/THA/61A/XXXX/G10P[5]: D13396 ; RVA/Cow-tc/USA/VMRI/XXXX/G6P[5]: U53923 ; RVA/Cow-tc/USA/WC3/1981/G6P[5]: AY050271 ; RVA/Cow-tc/GBR/678/XXXX/G8P[5]: D32054 ; RVA/Cow-tc/GBR/UK/1973/G6P[5]: M22306 ; RVA/Cow-tc/USA/B641/XXXX/G6P[5]: M63267 ; RVA/Cow-tc/USA/B223/XXXX/G10P[11]: M92986 .

    Article Snippet: 2.4 Sequence analyses A selection of reference strains available in the National Center for Biotechnology Information GenBank database ( http://www.ncbi.nlm.nih.gov/genbank/ ) was used for all sequence analyses.

    Techniques:

    Schematic representation of the G6P[5] partial VP7 deduced amino-acid sequence differences. Comparison was made from amino-acid number 9 through to amino-acid number 288 (total number of positions: 280), and only the diverging positions of G6P[5] strains from this study with the reference strain RVA/Cow-tc/GBR/UK/1973/G6P[5] (GenBank accession number: X00896 ) are shown. Black shade (■) indicates the amino-acid mutations only present in strains from one of the two groups of herds, dark grey shades ( and ) allow to highlight different amino-acid mutations at the same position shared by strains from both groups of herds and light grey shade ( ) indicates single amino-acid mutations shared by strains from both groups of herds. VR1 to VR8: Variable Region 1 to 8; (A–C): major antigenic region A–C.

    Journal: Vaccine

    Article Title: Impact of rotavirus vaccine on rotavirus genotypes and caliciviruses circulating in French cattle

    doi: 10.1016/j.vaccine.2013.03.039

    Figure Lengend Snippet: Schematic representation of the G6P[5] partial VP7 deduced amino-acid sequence differences. Comparison was made from amino-acid number 9 through to amino-acid number 288 (total number of positions: 280), and only the diverging positions of G6P[5] strains from this study with the reference strain RVA/Cow-tc/GBR/UK/1973/G6P[5] (GenBank accession number: X00896 ) are shown. Black shade (■) indicates the amino-acid mutations only present in strains from one of the two groups of herds, dark grey shades ( and ) allow to highlight different amino-acid mutations at the same position shared by strains from both groups of herds and light grey shade ( ) indicates single amino-acid mutations shared by strains from both groups of herds. VR1 to VR8: Variable Region 1 to 8; (A–C): major antigenic region A–C.

    Article Snippet: 2.4 Sequence analyses A selection of reference strains available in the National Center for Biotechnology Information GenBank database ( http://www.ncbi.nlm.nih.gov/genbank/ ) was used for all sequence analyses.

    Techniques: Sequencing

    Schematic representation of the G6P[5] partial VP4 deduced amino-acid sequence differences. Comparison was made from amino-acid number 51 through to amino-acid number 259 (total number of positions: 209), and only the diverging positions of G6P[5] strains from this study with the reference strain RVA/Cow-tc/GBR/UK/1973/G6P[5] (GenBank accession number: M22306 ) are shown. Black shade (■) indicates the amino-acid mutations only present in strains from one of the two groups of herds, dark grey shades ( and ) allow to highlight different amino-acid mutations at the same position shared by strains from both groups of herds and light grey shade ( ) indicates single amino-acid mutations shared by strains from both groups of herds. VR: Variable Region.

    Journal: Vaccine

    Article Title: Impact of rotavirus vaccine on rotavirus genotypes and caliciviruses circulating in French cattle

    doi: 10.1016/j.vaccine.2013.03.039

    Figure Lengend Snippet: Schematic representation of the G6P[5] partial VP4 deduced amino-acid sequence differences. Comparison was made from amino-acid number 51 through to amino-acid number 259 (total number of positions: 209), and only the diverging positions of G6P[5] strains from this study with the reference strain RVA/Cow-tc/GBR/UK/1973/G6P[5] (GenBank accession number: M22306 ) are shown. Black shade (■) indicates the amino-acid mutations only present in strains from one of the two groups of herds, dark grey shades ( and ) allow to highlight different amino-acid mutations at the same position shared by strains from both groups of herds and light grey shade ( ) indicates single amino-acid mutations shared by strains from both groups of herds. VR: Variable Region.

    Article Snippet: 2.4 Sequence analyses A selection of reference strains available in the National Center for Biotechnology Information GenBank database ( http://www.ncbi.nlm.nih.gov/genbank/ ) was used for all sequence analyses.

    Techniques: Sequencing

    Molecular phylogeny by Bayesian method obtained in a combined analysis using mitochondrial cytochrome oxidase I ( COI ) gene region (363 bp ), and H3 histone ( H3 ) gene fragment (330 bp ) sequences (a total of 693 positions in the final dataset) from Cryptorchestia and Orchestia species reported in Table 2 . Platorchestia platensis was used in this study as an outgroup species. Marked in blue: Cryptorchestia species; marked in green: Orchestia species. Numbers at nodes correspond to Bayesian posterior probability ( PP ) support values; PP values greater than 0.5 are labelled. The GenBank accession numbers of the DNA sequences from the COI and the histone H3 genes used in this study are reported in Table 2 .

    Journal: ZooKeys

    Article Title: On the molecular and morphological evolution of continental and insular Cryptorchestia species, with an additional description of C.garbinii ( Talitridae)

    doi: 10.3897/zookeys.783.26179

    Figure Lengend Snippet: Molecular phylogeny by Bayesian method obtained in a combined analysis using mitochondrial cytochrome oxidase I ( COI ) gene region (363 bp ), and H3 histone ( H3 ) gene fragment (330 bp ) sequences (a total of 693 positions in the final dataset) from Cryptorchestia and Orchestia species reported in Table 2 . Platorchestia platensis was used in this study as an outgroup species. Marked in blue: Cryptorchestia species; marked in green: Orchestia species. Numbers at nodes correspond to Bayesian posterior probability ( PP ) support values; PP values greater than 0.5 are labelled. The GenBank accession numbers of the DNA sequences from the COI and the histone H3 genes used in this study are reported in Table 2 .

    Article Snippet: The novel annotated sequences from the mt COI and the nuclear H3 genes from C. garbinii of this study have been submitted to the GenBank databases at the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov ) (Table ).

    Techniques:

    Phylogenetic analysis of 18S rRNA gene sequences (a) between Botryosphaeria laricina JAS6 and reference sequences; (b) Aspergillus tamarii JAS9 and reference sequences retrieved from NCBI GenBank constructed through neighbor joining method.

    Journal: PLoS ONE

    Article Title: Mycoremediation of Endosulfan and Its Metabolites in Aqueous Medium and Soil by Botryosphaeria laricina JAS6 and Aspergillus tamarii JAS9

    doi: 10.1371/journal.pone.0077170

    Figure Lengend Snippet: Phylogenetic analysis of 18S rRNA gene sequences (a) between Botryosphaeria laricina JAS6 and reference sequences; (b) Aspergillus tamarii JAS9 and reference sequences retrieved from NCBI GenBank constructed through neighbor joining method.

    Article Snippet: The sequencing result was submitted to the GenBank National Center for Biotechnology Information (NCBI) database.

    Techniques: Construct

    Multiple alignment of Bo_GH protein sequence vs . GH protein sequence at GenBank goat database

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

    doi: 10.1186/s43141-020-00046-6

    Figure Lengend Snippet: Multiple alignment of Bo_GH protein sequence vs . GH protein sequence at GenBank goat database

    Article Snippet: There are two alleles substitutions in Ossimi and Afghani sheep which yield a new codon that encodes for different amino acid; for Ossimi sheep, Gg472 c473 encodes for glycine (Gly, G), and Ca628 g629 encodes for glutamine (Gln, Q) for Afghani sheep, respectively compared to GTT for valine (Val, V) and CGC for arginine (Arg, R) in the GenBank database and in Afghani sheep, Gg389 c390 for glycine (Gly, G) compared to GTT for valine (Val, V) in the GenBank database.

    Techniques: Sequencing

    Motif patterns of As_GH protein sequence compared with GenBank database

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

    doi: 10.1186/s43141-020-00046-6

    Figure Lengend Snippet: Motif patterns of As_GH protein sequence compared with GenBank database

    Article Snippet: There are two alleles substitutions in Ossimi and Afghani sheep which yield a new codon that encodes for different amino acid; for Ossimi sheep, Gg472 c473 encodes for glycine (Gly, G), and Ca628 g629 encodes for glutamine (Gln, Q) for Afghani sheep, respectively compared to GTT for valine (Val, V) and CGC for arginine (Arg, R) in the GenBank database and in Afghani sheep, Gg389 c390 for glycine (Gly, G) compared to GTT for valine (Val, V) in the GenBank database.

    Techniques: Sequencing

    Multiple alignments of Assaf_GH cDNA sequences with GenBank sheep database

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

    doi: 10.1186/s43141-020-00046-6

    Figure Lengend Snippet: Multiple alignments of Assaf_GH cDNA sequences with GenBank sheep database

    Article Snippet: There are two alleles substitutions in Ossimi and Afghani sheep which yield a new codon that encodes for different amino acid; for Ossimi sheep, Gg472 c473 encodes for glycine (Gly, G), and Ca628 g629 encodes for glutamine (Gln, Q) for Afghani sheep, respectively compared to GTT for valine (Val, V) and CGC for arginine (Arg, R) in the GenBank database and in Afghani sheep, Gg389 c390 for glycine (Gly, G) compared to GTT for valine (Val, V) in the GenBank database.

    Techniques:

    Multiple alignment of conserved domain of Bo_GH protein residues with GenBank database

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

    doi: 10.1186/s43141-020-00046-6

    Figure Lengend Snippet: Multiple alignment of conserved domain of Bo_GH protein residues with GenBank database

    Article Snippet: There are two alleles substitutions in Ossimi and Afghani sheep which yield a new codon that encodes for different amino acid; for Ossimi sheep, Gg472 c473 encodes for glycine (Gly, G), and Ca628 g629 encodes for glutamine (Gln, Q) for Afghani sheep, respectively compared to GTT for valine (Val, V) and CGC for arginine (Arg, R) in the GenBank database and in Afghani sheep, Gg389 c390 for glycine (Gly, G) compared to GTT for valine (Val, V) in the GenBank database.

    Techniques:

    Multiple alignments of Boer_GH cDNA sequences with GenBank goat database

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

    doi: 10.1186/s43141-020-00046-6

    Figure Lengend Snippet: Multiple alignments of Boer_GH cDNA sequences with GenBank goat database

    Article Snippet: There are two alleles substitutions in Ossimi and Afghani sheep which yield a new codon that encodes for different amino acid; for Ossimi sheep, Gg472 c473 encodes for glycine (Gly, G), and Ca628 g629 encodes for glutamine (Gln, Q) for Afghani sheep, respectively compared to GTT for valine (Val, V) and CGC for arginine (Arg, R) in the GenBank database and in Afghani sheep, Gg389 c390 for glycine (Gly, G) compared to GTT for valine (Val, V) in the GenBank database.

    Techniques:

    Motif patterns of Bo_GH protein sequence compared with GenBank database

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

    doi: 10.1186/s43141-020-00046-6

    Figure Lengend Snippet: Motif patterns of Bo_GH protein sequence compared with GenBank database

    Article Snippet: There are two alleles substitutions in Ossimi and Afghani sheep which yield a new codon that encodes for different amino acid; for Ossimi sheep, Gg472 c473 encodes for glycine (Gly, G), and Ca628 g629 encodes for glutamine (Gln, Q) for Afghani sheep, respectively compared to GTT for valine (Val, V) and CGC for arginine (Arg, R) in the GenBank database and in Afghani sheep, Gg389 c390 for glycine (Gly, G) compared to GTT for valine (Val, V) in the GenBank database.

    Techniques: Sequencing

    Multiple alignment of conserved domain of As_GH protein residues with GenBank database

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

    doi: 10.1186/s43141-020-00046-6

    Figure Lengend Snippet: Multiple alignment of conserved domain of As_GH protein residues with GenBank database

    Article Snippet: There are two alleles substitutions in Ossimi and Afghani sheep which yield a new codon that encodes for different amino acid; for Ossimi sheep, Gg472 c473 encodes for glycine (Gly, G), and Ca628 g629 encodes for glutamine (Gln, Q) for Afghani sheep, respectively compared to GTT for valine (Val, V) and CGC for arginine (Arg, R) in the GenBank database and in Afghani sheep, Gg389 c390 for glycine (Gly, G) compared to GTT for valine (Val, V) in the GenBank database.

    Techniques:

    Multiple alignment of As_GH protein sequence vs. GH protein sequence at GenBank sheep database

    Journal: Journal of Genetic Engineering & Biotechnology

    Article Title: Cloning, nucleotide sequencing, and bioinformatics analyses of growth hormone mRNA of Assaf sheep and Boer goats reared in Egypt

    doi: 10.1186/s43141-020-00046-6

    Figure Lengend Snippet: Multiple alignment of As_GH protein sequence vs. GH protein sequence at GenBank sheep database

    Article Snippet: There are two alleles substitutions in Ossimi and Afghani sheep which yield a new codon that encodes for different amino acid; for Ossimi sheep, Gg472 c473 encodes for glycine (Gly, G), and Ca628 g629 encodes for glutamine (Gln, Q) for Afghani sheep, respectively compared to GTT for valine (Val, V) and CGC for arginine (Arg, R) in the GenBank database and in Afghani sheep, Gg389 c390 for glycine (Gly, G) compared to GTT for valine (Val, V) in the GenBank database.

    Techniques: Sequencing

    Nucleotide differences detected in 5'UTR sequences derived from patient PBMCs and plasma. Nucleotide changes in PBMC-derived IRES sequences (n=225) are indicated in blue while nucleoti de changes in plasma-derived IRES sequences (n=225) are indicated in red. Similarities in nucleotide frequency variation between PBMC and plasma-derived samples are represented in green dots while differences are represented in yellow dots. Structural domains are indicated in Roman letters (I-IV). The start codon AUG is highlighted in stem-loop domain IV. Substitution sites are indicated as squares and arrows indicate mutations described in the text. Nucleotide sequence and putative secondary RNA structure of the 5'UTR [nt. 1-383 genotype 1b (GenBank, AJ238799.1)] was adapted from Honda et al. [ 24 ].

    Journal: Advances in Virology

    Article Title: Quasispecies Changes with Distinctive Point Mutations in the Hepatitis C Virus Internal Ribosome Entry Site (IRES) Derived from PBMCs and Plasma

    doi: 10.1155/2018/4835252

    Figure Lengend Snippet: Nucleotide differences detected in 5'UTR sequences derived from patient PBMCs and plasma. Nucleotide changes in PBMC-derived IRES sequences (n=225) are indicated in blue while nucleoti de changes in plasma-derived IRES sequences (n=225) are indicated in red. Similarities in nucleotide frequency variation between PBMC and plasma-derived samples are represented in green dots while differences are represented in yellow dots. Structural domains are indicated in Roman letters (I-IV). The start codon AUG is highlighted in stem-loop domain IV. Substitution sites are indicated as squares and arrows indicate mutations described in the text. Nucleotide sequence and putative secondary RNA structure of the 5'UTR [nt. 1-383 genotype 1b (GenBank, AJ238799.1)] was adapted from Honda et al. [ 24 ].

    Article Snippet: As the majority of patients were infected with HCV subtype 1a the genomic sequences of 438 HCV subtype 1a isolates obtained from the Viral Bioinformatics Resource Centre database and GenBank were aligned with BioEdit software to align many HCV subtype 1a sequences in order to determine the most commonly expressed nucleotide at each position obtaining thus the best consensus sequence, which was used for multiple sequence alignments of PBMC and plasma-derived IRES amplicons.

    Techniques: Derivative Assay, Sequencing

    ( A ) Entry for cystic fibrosis, which contains links to the CFMDB and the list of CF cell lines available for research. ( B ) An example of links from the CFTR entry to Nomenclature, RefSeq, GenBank, Protein and UniGene databases.

    Journal: Nucleic Acids Research

    Article Title: Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

    doi:

    Figure Lengend Snippet: ( A ) Entry for cystic fibrosis, which contains links to the CFMDB and the list of CF cell lines available for research. ( B ) An example of links from the CFTR entry to Nomenclature, RefSeq, GenBank, Protein and UniGene databases.

    Article Snippet: Figure B shows an example of links from the CFTR entry to Nomenclature, RefSeq, GenBank, Protein and UniGene databases.

    Techniques:

    Alignment of the target sequences for probe sets 1370114_a_at and 1371776_at to the genomic sequence of rat chromosome 2. The arrowheads show the direction of transcription. Introns are not shown, and only the 3' end of the Pik3r1 sequence is shown. Target sequences were obtained from Affymetrix [7]. Transcript sequences were obtained from GenBank [28]. Genomic sequence of rat chromosome 2 and genomic alignments of the transcripts to the UCSC June 2003 rat assembly were obtained from UCSC Genome Bioinformatics [10].

    Journal: BMC Bioinformatics

    Article Title: Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

    doi: 10.1186/1471-2105-8-13

    Figure Lengend Snippet: Alignment of the target sequences for probe sets 1370114_a_at and 1371776_at to the genomic sequence of rat chromosome 2. The arrowheads show the direction of transcription. Introns are not shown, and only the 3' end of the Pik3r1 sequence is shown. Target sequences were obtained from Affymetrix [7]. Transcript sequences were obtained from GenBank [28]. Genomic sequence of rat chromosome 2 and genomic alignments of the transcripts to the UCSC June 2003 rat assembly were obtained from UCSC Genome Bioinformatics [10].

    Article Snippet: The first step is to map the GenBank accession numbers to LocusIDs by combining data available from LocusLink, UniGene and other sources of information.

    Techniques: Sequencing

    Alignment of the mRNAs for calcitonin (red) and CGRP (blue) to the genomic sequence (black line). The GenBank [28] accession numbers are given in parentheses. The coloured bars represent exons, with the narrower sections representing untranslated regions. The thin lines connecting the exons represent spliced out intronic regions. Genomic sequence was from the UCSC June 2003 rat assembly [10], and the alignments of the mRNAs to the genomic sequence were obtained from UCSC Genome Bioinformatics [10].

    Journal: BMC Bioinformatics

    Article Title: Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

    doi: 10.1186/1471-2105-8-13

    Figure Lengend Snippet: Alignment of the mRNAs for calcitonin (red) and CGRP (blue) to the genomic sequence (black line). The GenBank [28] accession numbers are given in parentheses. The coloured bars represent exons, with the narrower sections representing untranslated regions. The thin lines connecting the exons represent spliced out intronic regions. Genomic sequence was from the UCSC June 2003 rat assembly [10], and the alignments of the mRNAs to the genomic sequence were obtained from UCSC Genome Bioinformatics [10].

    Article Snippet: The first step is to map the GenBank accession numbers to LocusIDs by combining data available from LocusLink, UniGene and other sources of information.

    Techniques: Sequencing

    Onto-Tools integration (clockwise from top left). The user can analyze a set of differentially regulated genes using Onto-Express to find significantly affected biological processes. Onto-Compare can be used to find a suitable microarray for studying the hypotheses formulated based on these biological processes. If a suitable array is not found, Onto-Design can be used to design a custom array suitable for studying the hypotheses. One can refine the custom array design by creating the functional profile of the custom array and comparing it with the existing arrays. Once a suitable array is designed the user can either use Onto-Translate to obtain the list of GenBank accession numbers for the custom array or use Onto-Miner to obtain more details about each of the genes on the custom array such as the gene name, RefSeq accession number and chromosome location.

    Journal: Nucleic Acids Research

    Article Title: Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments

    doi: 10.1093/nar/gkh409

    Figure Lengend Snippet: Onto-Tools integration (clockwise from top left). The user can analyze a set of differentially regulated genes using Onto-Express to find significantly affected biological processes. Onto-Compare can be used to find a suitable microarray for studying the hypotheses formulated based on these biological processes. If a suitable array is not found, Onto-Design can be used to design a custom array suitable for studying the hypotheses. One can refine the custom array design by creating the functional profile of the custom array and comparing it with the existing arrays. Once a suitable array is designed the user can either use Onto-Translate to obtain the list of GenBank accession numbers for the custom array or use Onto-Miner to obtain more details about each of the genes on the custom array such as the gene name, RefSeq accession number and chromosome location.

    Article Snippet: For each organism, the user can search by clone ID, GenBank accession number, UniGene cluster ID, gene symbol, gene name or LocusLink ID.

    Techniques: Microarray, Functional Assay

    Measure of execution time (using GenBank database).

    Journal: The Scientific World Journal

    Article Title: An Improved Pearson's Correlation Proximity-Based Hierarchical Clustering for Mining Biological Association between Genes

    doi: 10.1155/2014/357873

    Figure Lengend Snippet: Measure of execution time (using GenBank database).

    Article Snippet: The GenBank sequence database contains the nucleotide sequences and their protein translations produced and maintained by the National Center for Biotechnology Information (NCBI) obtained from the URL ftp://ftp.ncbi.nih.gov/genbank/ , for experimental evaluation of the proposed PCPHC model with existing mining discriminative patterns for classifying trajectories, which extract the hidden and practical information from datasets.

    Techniques:

    Technique versus accuracy rate (using GenBank database).

    Journal: The Scientific World Journal

    Article Title: An Improved Pearson's Correlation Proximity-Based Hierarchical Clustering for Mining Biological Association between Genes

    doi: 10.1155/2014/357873

    Figure Lengend Snippet: Technique versus accuracy rate (using GenBank database).

    Article Snippet: The GenBank sequence database contains the nucleotide sequences and their protein translations produced and maintained by the National Center for Biotechnology Information (NCBI) obtained from the URL ftp://ftp.ncbi.nih.gov/genbank/ , for experimental evaluation of the proposed PCPHC model with existing mining discriminative patterns for classifying trajectories, which extract the hidden and practical information from datasets.

    Techniques:

    Representation of SkateBase data within the The National Center for Biotechnology Information (NCBI) databases. A . The little skate genome project is represented as a BioProject entry that connects all samples and data thematically. A BioSample record describes the DNA sample that was used for genome sequencing that was generated from a single stage 32 skate embryo. The SRA catalogs the unassembled Illumina genome sequence data. The Whole Genome Shotgun (WGS) database contains the contiguous sequences from shotgun sequencing projects. The assembled and annotated mitochondrial genome was deposited in GenBank and subsequently included in the NCBI Reference Sequence Database (RefSeq). B . The project to characterize the embryonic transcriptomes of L. erinacea , C. milii and S. canicula is represented in a BioProject entry. Three BioSample entries, one for each species, lead to three SRA datasets. The transcriptome data is represented also in the Gene Expression Omnibus (GEO), a database of high-throughput functional genomic data derived from microarrays and next-generation sequencing technologies.

    Journal: F1000Research

    Article Title: SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

    doi: 10.12688/f1000research.4996.1

    Figure Lengend Snippet: Representation of SkateBase data within the The National Center for Biotechnology Information (NCBI) databases. A . The little skate genome project is represented as a BioProject entry that connects all samples and data thematically. A BioSample record describes the DNA sample that was used for genome sequencing that was generated from a single stage 32 skate embryo. The SRA catalogs the unassembled Illumina genome sequence data. The Whole Genome Shotgun (WGS) database contains the contiguous sequences from shotgun sequencing projects. The assembled and annotated mitochondrial genome was deposited in GenBank and subsequently included in the NCBI Reference Sequence Database (RefSeq). B . The project to characterize the embryonic transcriptomes of L. erinacea , C. milii and S. canicula is represented in a BioProject entry. Three BioSample entries, one for each species, lead to three SRA datasets. The transcriptome data is represented also in the Gene Expression Omnibus (GEO), a database of high-throughput functional genomic data derived from microarrays and next-generation sequencing technologies.

    Article Snippet: The International Nucleotide Sequence Database Collaboration (INSDC) is composed of three large public nucleotide repositories, DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), and GenBank at the National Center for Biotechnology Information (NCBI).

    Techniques: Sequencing, Generated, Shotgun Sequencing, Expressing, High Throughput Screening Assay, Functional Assay, Derivative Assay, Next-Generation Sequencing

    GenBank and WGS data trends for Chondrichthyes and all taxa. GenBank is the National Institutes of Health (NIH) genetic sequence database and together with the DNA Databank of Japan (DDBJ) and the European Molecular Biological Laboratory (EMBL) comprise the International Nucleotide Sequence Database Collaboration (INSDC). The cumulative base pair total for all taxa as well as chondrichthyan only data are given versus time for GenBank and Whole Genome Shotgun (WGS) data. The Elephant Shark Genome Project is responsible for the spike in chondrichthyan GenBank in 2011. The little skate and elephant shark genome projects are currently the only two WGS datasets (yellow line).

    Journal: F1000Research

    Article Title: SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

    doi: 10.12688/f1000research.4996.1

    Figure Lengend Snippet: GenBank and WGS data trends for Chondrichthyes and all taxa. GenBank is the National Institutes of Health (NIH) genetic sequence database and together with the DNA Databank of Japan (DDBJ) and the European Molecular Biological Laboratory (EMBL) comprise the International Nucleotide Sequence Database Collaboration (INSDC). The cumulative base pair total for all taxa as well as chondrichthyan only data are given versus time for GenBank and Whole Genome Shotgun (WGS) data. The Elephant Shark Genome Project is responsible for the spike in chondrichthyan GenBank in 2011. The little skate and elephant shark genome projects are currently the only two WGS datasets (yellow line).

    Article Snippet: The International Nucleotide Sequence Database Collaboration (INSDC) is composed of three large public nucleotide repositories, DNA Data Bank of Japan (DDBJ), European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), and GenBank at the National Center for Biotechnology Information (NCBI).

    Techniques: Sequencing