blast database search Search Results


clc genomics workbench  (CLC Bio)
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intragenome blast  (Broad Institute Inc)
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blastn  (Paracel BLAST)
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gallus genome database  (Gallus BioPharmaceuticals)
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ncbi genbank blast similarity search program  (Biotechnology Information)
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tblastx  (Broad Institute Inc)
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genematcher™ software  (Paracel BLAST)
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Paracel BLAST genematcher™ software
Genematcher™ Software, supplied by Paracel BLAST, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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blastn and blastx algorithms  (Paracel BLAST)
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Paracel BLAST blastn and blastx algorithms
Workflow of the sequences analysis, from raw data to assignment.
Blastn And Blastx Algorithms, supplied by Paracel BLAST, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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c. neoformans predicted proteins  (Broad Institute Inc)
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Broad Institute Inc c. neoformans predicted proteins
C. <t> neoformans </t> strains used in these studies
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ncbi nucleotide database  (Biotechnology Information)
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C. <t> neoformans </t> strains used in these studies
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genbank database  (Biotechnology Information)
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Biotechnology Information genbank database
Phylogenetic tree of the msp4 partial gene (786 bp) of Anaplasma marginale haplotypes constructed in Bayesian inference (BI) analysis with MrBayes version 3.2 . The SYM + I model was chosen as the best-fitting nucleotide substitution model by JModelTest version 2.1.10 software [ , ]. The analysis was run for 2,000,000 generations, with 1,000,000 generations discarded as burn-in. Nodal support is indicated as Bayesian posterior probabilities. Sequences from A. centrale ( CP001759 ) and A. ovis ( KU497708 , KU497712 ) were used as outgroups. <t>GenBank</t> accession numbers, hosts, and countries of origin are shown. The sequences from this study are in bold. Am = A. marginale , Ao = A. ovis , Ac = A. centrale
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custom blast database spanning chic1 xist orthologous intervals  (Biotechnology Information)
86
Biotechnology Information custom blast database spanning chic1 xist orthologous intervals
Phylogenetic tree of the msp4 partial gene (786 bp) of Anaplasma marginale haplotypes constructed in Bayesian inference (BI) analysis with MrBayes version 3.2 . The SYM + I model was chosen as the best-fitting nucleotide substitution model by JModelTest version 2.1.10 software [ , ]. The analysis was run for 2,000,000 generations, with 1,000,000 generations discarded as burn-in. Nodal support is indicated as Bayesian posterior probabilities. Sequences from A. centrale ( CP001759 ) and A. ovis ( KU497708 , KU497712 ) were used as outgroups. <t>GenBank</t> accession numbers, hosts, and countries of origin are shown. The sequences from this study are in bold. Am = A. marginale , Ao = A. ovis , Ac = A. centrale
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Image Search Results


Workflow of the sequences analysis, from raw data to assignment.

Journal: PLoS ONE

Article Title: Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

doi: 10.1371/journal.pone.0038499

Figure Lengend Snippet: Workflow of the sequences analysis, from raw data to assignment.

Article Snippet: The aforementioned databases were scanned using the BlastN and BlastX algorithms provided by Paracel Blast (Striking Development), a software capable of executing searches on multiple non-shared-memory processors simultaneously.

Techniques: Sequencing

C. neoformans strains used in these studies

Journal: Glycobiology

Article Title: Cryptococcus neoformans UGT1 encodes a UDP-Galactose/UDP-GalNAc transporter

doi: 10.1093/glycob/cww078

Figure Lengend Snippet: C. neoformans strains used in these studies

Article Snippet: UGT1 was identified by BLASTP searches against C. neoformans predicted proteins (Broad Institute; C. neoformans var. grubii H99 database) using known UDP-galactose transporters from Schizosaccharomyces pombe ( {"type":"entrez-protein","attrs":{"text":"NP_588041","term_id":"19075541","term_text":"NP_588041"}} NP_588041 ), Arabidopsis thaliana ( {"type":"entrez-protein","attrs":{"text":"NP_565158.1","term_id":"18411611","term_text":"NP_565158.1"}} NP_565158.1 ), Caenorhabditis elegans ( {"type":"entrez-protein","attrs":{"text":"NP_001255676.1","term_id":"392901327","term_text":"NP_001255676.1"}} NP_001255676.1 ) and Homo sapiens ( {"type":"entrez-nucleotide","attrs":{"text":"NC_000023.11","term_id":"568815575","term_text":"NC_000023.11"}} NC_000023.11 ).

Techniques:

Topology of C. neoformans Ugt1 as predicted by TMHMM server v 2.0, showing 10 putative transmembrane domains and long N- and C-terminal cytosolic tails. Arrowheads indicate the new N-terminus for each N-terminal truncation and the terminal residue of the single C-terminal truncation (C1); see text and Table III for details.

Journal: Glycobiology

Article Title: Cryptococcus neoformans UGT1 encodes a UDP-Galactose/UDP-GalNAc transporter

doi: 10.1093/glycob/cww078

Figure Lengend Snippet: Topology of C. neoformans Ugt1 as predicted by TMHMM server v 2.0, showing 10 putative transmembrane domains and long N- and C-terminal cytosolic tails. Arrowheads indicate the new N-terminus for each N-terminal truncation and the terminal residue of the single C-terminal truncation (C1); see text and Table III for details.

Article Snippet: UGT1 was identified by BLASTP searches against C. neoformans predicted proteins (Broad Institute; C. neoformans var. grubii H99 database) using known UDP-galactose transporters from Schizosaccharomyces pombe ( {"type":"entrez-protein","attrs":{"text":"NP_588041","term_id":"19075541","term_text":"NP_588041"}} NP_588041 ), Arabidopsis thaliana ( {"type":"entrez-protein","attrs":{"text":"NP_565158.1","term_id":"18411611","term_text":"NP_565158.1"}} NP_565158.1 ), Caenorhabditis elegans ( {"type":"entrez-protein","attrs":{"text":"NP_001255676.1","term_id":"392901327","term_text":"NP_001255676.1"}} NP_001255676.1 ) and Homo sapiens ( {"type":"entrez-nucleotide","attrs":{"text":"NC_000023.11","term_id":"568815575","term_text":"NC_000023.11"}} NC_000023.11 ).

Techniques: Residue

Cells lacking Ugt1 are more efficiently phagocytosed and killed by THP-1 cells than wild-type C. neoformans. (A) Phagocytic index (engulfed fungi/100 host cells) of strains grown in YPD (−/+ opsonization) or in inducing media (+ opsonization). (B) Survival of YPD-grown, opsonized fungi after internalization by THP-1 cells. Data are representative of three independent experiments performed with n = 3 (*, P < 0.01; **, P < 0.001).

Journal: Glycobiology

Article Title: Cryptococcus neoformans UGT1 encodes a UDP-Galactose/UDP-GalNAc transporter

doi: 10.1093/glycob/cww078

Figure Lengend Snippet: Cells lacking Ugt1 are more efficiently phagocytosed and killed by THP-1 cells than wild-type C. neoformans. (A) Phagocytic index (engulfed fungi/100 host cells) of strains grown in YPD (−/+ opsonization) or in inducing media (+ opsonization). (B) Survival of YPD-grown, opsonized fungi after internalization by THP-1 cells. Data are representative of three independent experiments performed with n = 3 (*, P < 0.01; **, P < 0.001).

Article Snippet: UGT1 was identified by BLASTP searches against C. neoformans predicted proteins (Broad Institute; C. neoformans var. grubii H99 database) using known UDP-galactose transporters from Schizosaccharomyces pombe ( {"type":"entrez-protein","attrs":{"text":"NP_588041","term_id":"19075541","term_text":"NP_588041"}} NP_588041 ), Arabidopsis thaliana ( {"type":"entrez-protein","attrs":{"text":"NP_565158.1","term_id":"18411611","term_text":"NP_565158.1"}} NP_565158.1 ), Caenorhabditis elegans ( {"type":"entrez-protein","attrs":{"text":"NP_001255676.1","term_id":"392901327","term_text":"NP_001255676.1"}} NP_001255676.1 ) and Homo sapiens ( {"type":"entrez-nucleotide","attrs":{"text":"NC_000023.11","term_id":"568815575","term_text":"NC_000023.11"}} NC_000023.11 ).

Techniques:

Phylogenetic tree of the msp4 partial gene (786 bp) of Anaplasma marginale haplotypes constructed in Bayesian inference (BI) analysis with MrBayes version 3.2 . The SYM + I model was chosen as the best-fitting nucleotide substitution model by JModelTest version 2.1.10 software [ , ]. The analysis was run for 2,000,000 generations, with 1,000,000 generations discarded as burn-in. Nodal support is indicated as Bayesian posterior probabilities. Sequences from A. centrale ( CP001759 ) and A. ovis ( KU497708 , KU497712 ) were used as outgroups. GenBank accession numbers, hosts, and countries of origin are shown. The sequences from this study are in bold. Am = A. marginale , Ao = A. ovis , Ac = A. centrale

Journal: Parasites & Vectors

Article Title: First report of Anaplasma marginale in the European bison Bison bonasus

doi: 10.1186/s13071-025-07056-8

Figure Lengend Snippet: Phylogenetic tree of the msp4 partial gene (786 bp) of Anaplasma marginale haplotypes constructed in Bayesian inference (BI) analysis with MrBayes version 3.2 . The SYM + I model was chosen as the best-fitting nucleotide substitution model by JModelTest version 2.1.10 software [ , ]. The analysis was run for 2,000,000 generations, with 1,000,000 generations discarded as burn-in. Nodal support is indicated as Bayesian posterior probabilities. Sequences from A. centrale ( CP001759 ) and A. ovis ( KU497708 , KU497712 ) were used as outgroups. GenBank accession numbers, hosts, and countries of origin are shown. The sequences from this study are in bold. Am = A. marginale , Ao = A. ovis , Ac = A. centrale

Article Snippet: The obtained sequences were compared with the GenBank database (Basic Local Alignment Search Tool [BLAST], National Center for Biotechnology Information [NCBI], USA) and then submitted to GenBank.

Techniques: Construct, Software