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Pacific Biosciences open reading frame
Open Reading Frame, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Mass Spectrometry:

Article Title: Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing
Article Snippet: .. For MS searching, a customized protein search database was constructed, consisting of protein sequences derived from Gencode v19 (95,309 entries), ORFs predicted from MCF-7 PacBio sequences (47,325 entries), and a database of frequently observed contaminant proteins (115 entries) [ , ]. .. The inclusion of the Gencode database allows for identification of any peptides derived from transcripts that may not have been detected in the PacBio data.

other:

Article Title: A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing
Article Snippet: When considering only retained ORFs from TransDecoder in both datasets, 80.8% of PacBio ORFs and 70% of de novo ORFs mapped to the sorghum genome.

RNA Sequencing Assay:

Article Title: Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus
Article Snippet: .. Even though the number of predicted ORFs in the PacBio dataset was less than that in the de novo dataset, the full-length transcripts included longer coding transcripts (26,683 ORFs with average length of 1457 bp) while the average length of ORFs in assembled transcripts was only 661 bp in the previous RNA-seq study of M . anguillicaudatus . ..

Article Title: Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus
Article Snippet: .. Even though the number of predicted ORFs in the PacBio dataset was less than that in the de novo dataset, the full-length transcripts included longer coding transcripts (26,683 ORFs with average length of 1457 bp) while the average length of ORFs in assembled transcripts was only 661 bp in the previous RNA-seq study of M . anguillicaudatus . ..

Construct:

Article Title: Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing
Article Snippet: .. For MS searching, a customized protein search database was constructed, consisting of protein sequences derived from Gencode v19 (95,309 entries), ORFs predicted from MCF-7 PacBio sequences (47,325 entries), and a database of frequently observed contaminant proteins (115 entries) [ , ]. .. The inclusion of the Gencode database allows for identification of any peptides derived from transcripts that may not have been detected in the PacBio data.

Derivative Assay:

Article Title: Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing
Article Snippet: .. For MS searching, a customized protein search database was constructed, consisting of protein sequences derived from Gencode v19 (95,309 entries), ORFs predicted from MCF-7 PacBio sequences (47,325 entries), and a database of frequently observed contaminant proteins (115 entries) [ , ]. .. The inclusion of the Gencode database allows for identification of any peptides derived from transcripts that may not have been detected in the PacBio data.

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  • 90
    Pacific Biosciences pacbio data
    Identification of AS events. a The number distribution of AS events in loci detected by the <t>PacBio</t> Sequel platform. b Distribution of loci that produce two or more splice <t>isoforms</t> detected by the PacBio Sequel platform
    Pacbio Data, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pacbio data/product/Pacific Biosciences
    Average 90 stars, based on 2 article reviews
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    90/100 stars
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    94
    Pacific Biosciences transcription start site tiss data
    Analysis of viral transcription start sites <t>(TiSS).</t> a Screenshot of our HSV-1 viewer displaying the annotated mRNAs of MinION, PacBio and coverage of read 5’-ends for <t>cRNA-seq</t> and dRNA-seq of the UL22.5-UL25 gene locus. Transcripts in our reference annotation are indicated in blue. b , c Venn diagram depicting the number of Transcription start sites (TiSS) that were identified by cRNA-seq, dRNA-seq and MinION 14 ( b ) or PacBio 13 ( c ) sequencing, respectively. TiSS included into the final annotation are indicated by the black circle. d Histogram depicting the number of TiSS criteria that were fulfilled by the individual viral transcripts. e Sequence logos upstream of viral TiSS with viral TiSS grouped into three equally sized bins according to their transcription rates (top: highest; bottom: lowest). The TATA-box and initiator element (Inr) are shown. f Log fold-change between cytoplasmic and chromatin-associated FPKM-normalized read counts (export index) of cellular (gray) and viral (red and blue) gene clusters compared between wild-type HSV-1 (wt) and a null mutant of the viral RNA export factor ICP27 (ΔICP27). Viral immediate early genes are indicated in blue.
    Transcription Start Site Tiss Data, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 94/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/transcription start site tiss data/product/Pacific Biosciences
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    90
    Pacific Biosciences c freundii b38
    Class 1 integrons identified on pOZ172 and pOZ181 in C. <t>freundii</t> <t>B38</t> and related plasmids. (A) Tn 6017 , a Tn 402 / 5053 -like integron, was identified on pOZ172 and was inserted into the res II site of Tn 1722 , splitting the res site into two half res . Arrow boxes show the genes and their orientations; each solid black oval indicates attI , and each white oval represents the attC of the preceding gene. Δ, disrupted genes. mcp is the gene for the methyl-accepting chemotaxis protein of Tn 1722 . (B) The two most representative sul1 -type bla IMP-4 class 1 integrons found in GenBank. Their cassette arrays are the same but differ from that of Tn 6017 . The black rectangle is 25-nt repeat IRi; the short vertical lines are the 12-nt repeats of IS 26 . (C) A second, sul1 -type integron was identified on pOZ181 and was linked upstream to Tn 1696 and downstream to an IS CR1 . The small rectangular white boxes represent the res sites adjacent to tnpR , and the solid black boxes represent the 25-bp IRi (Tn 402 ) and IRt (Tn 5053 ) sites; the larger solid black boxes represent the 38-bp IRL and IRRI of Tn 1722 , as well as IRtnp of Tn 1696 . The small arrows represent the direction of promoters (P and P1).
    C Freundii B38, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/c freundii b38/product/Pacific Biosciences
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    93
    Pacific Biosciences isoforms
    Identification of AS events. a The number distribution of AS events in loci detected by the PacBio Sequel platform. b Distribution of loci that produce two or more splice <t>isoforms</t> detected by the PacBio Sequel platform
    Isoforms, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 69 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/isoforms/product/Pacific Biosciences
    Average 93 stars, based on 69 article reviews
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    isoforms - by Bioz Stars, 2020-09
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    Image Search Results


    Identification of AS events. a The number distribution of AS events in loci detected by the PacBio Sequel platform. b Distribution of loci that produce two or more splice isoforms detected by the PacBio Sequel platform

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: Identification of AS events. a The number distribution of AS events in loci detected by the PacBio Sequel platform. b Distribution of loci that produce two or more splice isoforms detected by the PacBio Sequel platform

    Article Snippet: LncRNA and ORF identification To identify LncRNA, novel isoforms from known genes or novel isoforms from novel genes obtained by PacBio data were first searched against NR, KOG, KO, and Swiss-Prot databases with default parameters.

    Techniques:

    Isoform length density and Isoform number of loci density. a The length distribution of all isoforms in the PacBio Sequel platform compared to the reference genome. b The number distribution of isoforms from each locus in the PacBio Sequel platform compared to the reference genome

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: Isoform length density and Isoform number of loci density. a The length distribution of all isoforms in the PacBio Sequel platform compared to the reference genome. b The number distribution of isoforms from each locus in the PacBio Sequel platform compared to the reference genome

    Article Snippet: LncRNA and ORF identification To identify LncRNA, novel isoforms from known genes or novel isoforms from novel genes obtained by PacBio data were first searched against NR, KOG, KO, and Swiss-Prot databases with default parameters.

    Techniques:

    Circos visualization of the PacBio Sequel platform at genome-wide level. a Ten chromosomes distribution of B.rapa genome. b APA sites distribution mapped to B.rapa genome. c Novel isoforms density from the PacBio Sequel platform. d Novel loci density from the PacBio Sequel platform. The closer the color is to red, the higher the density. Conversely, the closer the color is to blue, the lower the density. e LncRNA density from the PacBio Sequel platform. The closer the point is to the center, the lower the density. f Fusion transcripts distribution. Purple line represents intra-chromosome fusion transcripts, and yellow line represents inter-chromosomal

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: Circos visualization of the PacBio Sequel platform at genome-wide level. a Ten chromosomes distribution of B.rapa genome. b APA sites distribution mapped to B.rapa genome. c Novel isoforms density from the PacBio Sequel platform. d Novel loci density from the PacBio Sequel platform. The closer the color is to red, the higher the density. Conversely, the closer the color is to blue, the lower the density. e LncRNA density from the PacBio Sequel platform. The closer the point is to the center, the lower the density. f Fusion transcripts distribution. Purple line represents intra-chromosome fusion transcripts, and yellow line represents inter-chromosomal

    Article Snippet: LncRNA and ORF identification To identify LncRNA, novel isoforms from known genes or novel isoforms from novel genes obtained by PacBio data were first searched against NR, KOG, KO, and Swiss-Prot databases with default parameters.

    Techniques: Genome Wide

    Function annotations of novel isoforms identified by the PacBio Sequel platform. a The number statistics of novel isoforms in Nr, GO, KEGG, KOG databases. b Distribution of novel isoforms in Nr homologous top 20 species. c Distribution of novel isoforms in GO terms. d Distribution of novel isoforms in KEGG pathway. e Distribution of novel isoforms in KOG

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: Function annotations of novel isoforms identified by the PacBio Sequel platform. a The number statistics of novel isoforms in Nr, GO, KEGG, KOG databases. b Distribution of novel isoforms in Nr homologous top 20 species. c Distribution of novel isoforms in GO terms. d Distribution of novel isoforms in KEGG pathway. e Distribution of novel isoforms in KOG

    Article Snippet: LncRNA and ORF identification To identify LncRNA, novel isoforms from known genes or novel isoforms from novel genes obtained by PacBio data were first searched against NR, KOG, KO, and Swiss-Prot databases with default parameters.

    Techniques:

    Analysis of viral transcription start sites (TiSS). a Screenshot of our HSV-1 viewer displaying the annotated mRNAs of MinION, PacBio and coverage of read 5’-ends for cRNA-seq and dRNA-seq of the UL22.5-UL25 gene locus. Transcripts in our reference annotation are indicated in blue. b , c Venn diagram depicting the number of Transcription start sites (TiSS) that were identified by cRNA-seq, dRNA-seq and MinION 14 ( b ) or PacBio 13 ( c ) sequencing, respectively. TiSS included into the final annotation are indicated by the black circle. d Histogram depicting the number of TiSS criteria that were fulfilled by the individual viral transcripts. e Sequence logos upstream of viral TiSS with viral TiSS grouped into three equally sized bins according to their transcription rates (top: highest; bottom: lowest). The TATA-box and initiator element (Inr) are shown. f Log fold-change between cytoplasmic and chromatin-associated FPKM-normalized read counts (export index) of cellular (gray) and viral (red and blue) gene clusters compared between wild-type HSV-1 (wt) and a null mutant of the viral RNA export factor ICP27 (ΔICP27). Viral immediate early genes are indicated in blue.

    Journal: Nature Communications

    Article Title: Integrative functional genomics decodes herpes simplex virus 1

    doi: 10.1038/s41467-020-15992-5

    Figure Lengend Snippet: Analysis of viral transcription start sites (TiSS). a Screenshot of our HSV-1 viewer displaying the annotated mRNAs of MinION, PacBio and coverage of read 5’-ends for cRNA-seq and dRNA-seq of the UL22.5-UL25 gene locus. Transcripts in our reference annotation are indicated in blue. b , c Venn diagram depicting the number of Transcription start sites (TiSS) that were identified by cRNA-seq, dRNA-seq and MinION 14 ( b ) or PacBio 13 ( c ) sequencing, respectively. TiSS included into the final annotation are indicated by the black circle. d Histogram depicting the number of TiSS criteria that were fulfilled by the individual viral transcripts. e Sequence logos upstream of viral TiSS with viral TiSS grouped into three equally sized bins according to their transcription rates (top: highest; bottom: lowest). The TATA-box and initiator element (Inr) are shown. f Log fold-change between cytoplasmic and chromatin-associated FPKM-normalized read counts (export index) of cellular (gray) and viral (red and blue) gene clusters compared between wild-type HSV-1 (wt) and a null mutant of the viral RNA export factor ICP27 (ΔICP27). Viral immediate early genes are indicated in blue.

    Article Snippet: Integrative analysis of transcription start site (TiSS) data obtained by both second (cRNA-seq, dRNA-seq) and third (PacBio, MinION) generation sequencing approaches highlighted the necessity to validate viral TiSS by multiple means to exclude such experimental artifacts generated by the individual approaches.

    Techniques: Sequencing, Mutagenesis

    Class 1 integrons identified on pOZ172 and pOZ181 in C. freundii B38 and related plasmids. (A) Tn 6017 , a Tn 402 / 5053 -like integron, was identified on pOZ172 and was inserted into the res II site of Tn 1722 , splitting the res site into two half res . Arrow boxes show the genes and their orientations; each solid black oval indicates attI , and each white oval represents the attC of the preceding gene. Δ, disrupted genes. mcp is the gene for the methyl-accepting chemotaxis protein of Tn 1722 . (B) The two most representative sul1 -type bla IMP-4 class 1 integrons found in GenBank. Their cassette arrays are the same but differ from that of Tn 6017 . The black rectangle is 25-nt repeat IRi; the short vertical lines are the 12-nt repeats of IS 26 . (C) A second, sul1 -type integron was identified on pOZ181 and was linked upstream to Tn 1696 and downstream to an IS CR1 . The small rectangular white boxes represent the res sites adjacent to tnpR , and the solid black boxes represent the 25-bp IRi (Tn 402 ) and IRt (Tn 5053 ) sites; the larger solid black boxes represent the 38-bp IRL and IRRI of Tn 1722 , as well as IRtnp of Tn 1696 . The small arrows represent the direction of promoters (P and P1).

    Journal: Antimicrobial Agents and Chemotherapy

    Article Title: Genome and Plasmid Analysis of blaIMP-4-Carrying Citrobacter freundii B38

    doi: 10.1128/AAC.00588-16

    Figure Lengend Snippet: Class 1 integrons identified on pOZ172 and pOZ181 in C. freundii B38 and related plasmids. (A) Tn 6017 , a Tn 402 / 5053 -like integron, was identified on pOZ172 and was inserted into the res II site of Tn 1722 , splitting the res site into two half res . Arrow boxes show the genes and their orientations; each solid black oval indicates attI , and each white oval represents the attC of the preceding gene. Δ, disrupted genes. mcp is the gene for the methyl-accepting chemotaxis protein of Tn 1722 . (B) The two most representative sul1 -type bla IMP-4 class 1 integrons found in GenBank. Their cassette arrays are the same but differ from that of Tn 6017 . The black rectangle is 25-nt repeat IRi; the short vertical lines are the 12-nt repeats of IS 26 . (C) A second, sul1 -type integron was identified on pOZ181 and was linked upstream to Tn 1696 and downstream to an IS CR1 . The small rectangular white boxes represent the res sites adjacent to tnpR , and the solid black boxes represent the 25-bp IRi (Tn 402 ) and IRt (Tn 5053 ) sites; the larger solid black boxes represent the 38-bp IRL and IRRI of Tn 1722 , as well as IRtnp of Tn 1696 . The small arrows represent the direction of promoters (P and P1).

    Article Snippet: The bla IMP-4 -carrying class 1 integron in pOZ172 plasmid in C. freundii B38 contained four cassettes ( bla IMP-4 - qacG2-aacA4 - aphA15 ) and a complete but hybrid tni module ( tniR-tniQ-tniB-tniA ) composed of tniR from Tn 402 (identical) and tniQ-tniB-tniA from Tn 5053 (6-nucleotide [nt] difference) ( ).

    Techniques: Chemotaxis Assay

    Identification of AS events. a The number distribution of AS events in loci detected by the PacBio Sequel platform. b Distribution of loci that produce two or more splice isoforms detected by the PacBio Sequel platform

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: Identification of AS events. a The number distribution of AS events in loci detected by the PacBio Sequel platform. b Distribution of loci that produce two or more splice isoforms detected by the PacBio Sequel platform

    Article Snippet: The novel isoforms from novel genes and novel isoforms from known genes with no hit in the above functional annotation databases, were predicted by CPAT software to identify lncRNAs in the PacBio data set.

    Techniques:

    Isoform length density and Isoform number of loci density. a The length distribution of all isoforms in the PacBio Sequel platform compared to the reference genome. b The number distribution of isoforms from each locus in the PacBio Sequel platform compared to the reference genome

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: Isoform length density and Isoform number of loci density. a The length distribution of all isoforms in the PacBio Sequel platform compared to the reference genome. b The number distribution of isoforms from each locus in the PacBio Sequel platform compared to the reference genome

    Article Snippet: The novel isoforms from novel genes and novel isoforms from known genes with no hit in the above functional annotation databases, were predicted by CPAT software to identify lncRNAs in the PacBio data set.

    Techniques:

    LncRNA and ORF analysis. a Identification of four types of lncRNA. b Number, percentage and length distributions of CDS of novel isoforms with predicted ORF. c Number, percentage and length distributions of 3′ UTRs of novel isoforms with predicted ORF. d Number, percentage and length distributions of 5′ UTRs of novel isoforms with predicted ORF. e Exon number distribution of novel isoforms with predicted ORF and lncRNAs

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: LncRNA and ORF analysis. a Identification of four types of lncRNA. b Number, percentage and length distributions of CDS of novel isoforms with predicted ORF. c Number, percentage and length distributions of 3′ UTRs of novel isoforms with predicted ORF. d Number, percentage and length distributions of 5′ UTRs of novel isoforms with predicted ORF. e Exon number distribution of novel isoforms with predicted ORF and lncRNAs

    Article Snippet: The novel isoforms from novel genes and novel isoforms from known genes with no hit in the above functional annotation databases, were predicted by CPAT software to identify lncRNAs in the PacBio data set.

    Techniques:

    Circos visualization of the PacBio Sequel platform at genome-wide level. a Ten chromosomes distribution of B.rapa genome. b APA sites distribution mapped to B.rapa genome. c Novel isoforms density from the PacBio Sequel platform. d Novel loci density from the PacBio Sequel platform. The closer the color is to red, the higher the density. Conversely, the closer the color is to blue, the lower the density. e LncRNA density from the PacBio Sequel platform. The closer the point is to the center, the lower the density. f Fusion transcripts distribution. Purple line represents intra-chromosome fusion transcripts, and yellow line represents inter-chromosomal

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: Circos visualization of the PacBio Sequel platform at genome-wide level. a Ten chromosomes distribution of B.rapa genome. b APA sites distribution mapped to B.rapa genome. c Novel isoforms density from the PacBio Sequel platform. d Novel loci density from the PacBio Sequel platform. The closer the color is to red, the higher the density. Conversely, the closer the color is to blue, the lower the density. e LncRNA density from the PacBio Sequel platform. The closer the point is to the center, the lower the density. f Fusion transcripts distribution. Purple line represents intra-chromosome fusion transcripts, and yellow line represents inter-chromosomal

    Article Snippet: The novel isoforms from novel genes and novel isoforms from known genes with no hit in the above functional annotation databases, were predicted by CPAT software to identify lncRNAs in the PacBio data set.

    Techniques: Genome Wide

    Function annotations of novel isoforms identified by the PacBio Sequel platform. a The number statistics of novel isoforms in Nr, GO, KEGG, KOG databases. b Distribution of novel isoforms in Nr homologous top 20 species. c Distribution of novel isoforms in GO terms. d Distribution of novel isoforms in KEGG pathway. e Distribution of novel isoforms in KOG

    Journal: BMC Plant Biology

    Article Title: Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

    doi: 10.1186/s12870-019-2133-z

    Figure Lengend Snippet: Function annotations of novel isoforms identified by the PacBio Sequel platform. a The number statistics of novel isoforms in Nr, GO, KEGG, KOG databases. b Distribution of novel isoforms in Nr homologous top 20 species. c Distribution of novel isoforms in GO terms. d Distribution of novel isoforms in KEGG pathway. e Distribution of novel isoforms in KOG

    Article Snippet: The novel isoforms from novel genes and novel isoforms from known genes with no hit in the above functional annotation databases, were predicted by CPAT software to identify lncRNAs in the PacBio data set.

    Techniques: