SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss
SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and...
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ftpubmed:oai:pubmedcentral.nih.gov:3225076 2023-05-15T18:09:45+02:00 SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss Di Génova, Alex Aravena, Andrés Zapata, Luis González, Mauricio Maass, Alejandro Iturra, Patricia 2011-11-25 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225076 http://www.ncbi.nlm.nih.gov/pubmed/22120661 https://doi.org/10.1093/database/bar050 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225076 http://www.ncbi.nlm.nih.gov/pubmed/22120661 http://dx.doi.org/10.1093/database/bar050 © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. CC-BY-NC Original Article Text 2011 ftpubmed https://doi.org/10.1093/database/bar050 2013-09-03T23:08:23Z SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Text Salmo salar PubMed Central (PMC) Database 2011 0 bar050 bar050 |
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Original Article Di Génova, Alex Aravena, Andrés Zapata, Luis González, Mauricio Maass, Alejandro Iturra, Patricia SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss |
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Original Article |
description |
SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. |
format |
Text |
author |
Di Génova, Alex Aravena, Andrés Zapata, Luis González, Mauricio Maass, Alejandro Iturra, Patricia |
author_facet |
Di Génova, Alex Aravena, Andrés Zapata, Luis González, Mauricio Maass, Alejandro Iturra, Patricia |
author_sort |
Di Génova, Alex |
title |
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss |
title_short |
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss |
title_full |
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss |
title_fullStr |
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss |
title_full_unstemmed |
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss |
title_sort |
salmondb: a bioinformatics resource for salmo salar and oncorhynchus mykiss |
publisher |
Oxford University Press |
publishDate |
2011 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225076 http://www.ncbi.nlm.nih.gov/pubmed/22120661 https://doi.org/10.1093/database/bar050 |
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Salmo salar |
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Salmo salar |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225076 http://www.ncbi.nlm.nih.gov/pubmed/22120661 http://dx.doi.org/10.1093/database/bar050 |
op_rights |
© The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
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https://doi.org/10.1093/database/bar050 |
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