Roundup 2.0: enabling comparative genomics for over 1800 genomes

Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based...

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Detalles Bibliográficos
Autores principales: DeLuca, Todd F., Cui, Jike, Jung, Jae-Yoon, St. Gabriel, Kristian Che, Wall, Dennis P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289913/
https://www.ncbi.nlm.nih.gov/pubmed/22247275
http://dx.doi.org/10.1093/bioinformatics/bts006
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author DeLuca, Todd F.
Cui, Jike
Jung, Jae-Yoon
St. Gabriel, Kristian Che
Wall, Dennis P.
author_facet DeLuca, Todd F.
Cui, Jike
Jung, Jae-Yoon
St. Gabriel, Kristian Che
Wall, Dennis P.
author_sort DeLuca, Todd F.
collection PubMed
description Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available. Availability: http://roundup.hms.harvard.edu Contact: dpwall@hms.harvard.edu; todd_deluca@hms.harvard.edu
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spelling pubmed-32899132012-02-29 Roundup 2.0: enabling comparative genomics for over 1800 genomes DeLuca, Todd F. Cui, Jike Jung, Jae-Yoon St. Gabriel, Kristian Che Wall, Dennis P. Bioinformatics Applications Note Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available. Availability: http://roundup.hms.harvard.edu Contact: dpwall@hms.harvard.edu; todd_deluca@hms.harvard.edu Oxford University Press 2012-03-01 2012-01-13 /pmc/articles/PMC3289913/ /pubmed/22247275 http://dx.doi.org/10.1093/bioinformatics/bts006 Text en © The Author(s) 2012. 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.
spellingShingle Applications Note
DeLuca, Todd F.
Cui, Jike
Jung, Jae-Yoon
St. Gabriel, Kristian Che
Wall, Dennis P.
Roundup 2.0: enabling comparative genomics for over 1800 genomes
title Roundup 2.0: enabling comparative genomics for over 1800 genomes
title_full Roundup 2.0: enabling comparative genomics for over 1800 genomes
title_fullStr Roundup 2.0: enabling comparative genomics for over 1800 genomes
title_full_unstemmed Roundup 2.0: enabling comparative genomics for over 1800 genomes
title_short Roundup 2.0: enabling comparative genomics for over 1800 genomes
title_sort roundup 2.0: enabling comparative genomics for over 1800 genomes
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289913/
https://www.ncbi.nlm.nih.gov/pubmed/22247275
http://dx.doi.org/10.1093/bioinformatics/bts006
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