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ISfinder: the reference centre for bacterial insertion sequences

ISfinder () is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with i...

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Detalles Bibliográficos
Autores principales: Siguier, P., Perochon, J., Lestrade, L., Mahillon, J., Chandler, M.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347377/
https://www.ncbi.nlm.nih.gov/pubmed/16381877
http://dx.doi.org/10.1093/nar/gkj014
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author Siguier, P.
Perochon, J.
Lestrade, L.
Mahillon, J.
Chandler, M.
author_facet Siguier, P.
Perochon, J.
Lestrade, L.
Mahillon, J.
Chandler, M.
author_sort Siguier, P.
collection PubMed
description ISfinder () is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.
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spelling pubmed-13473772006-01-25 ISfinder: the reference centre for bacterial insertion sequences Siguier, P. Perochon, J. Lestrade, L. Mahillon, J. Chandler, M. Nucleic Acids Res Article ISfinder () is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication. Oxford University Press 2006-01-01 2005-12-28 /pmc/articles/PMC1347377/ /pubmed/16381877 http://dx.doi.org/10.1093/nar/gkj014 Text en © The Author 2006. Published by Oxford University Press. All rights reserved
spellingShingle Article
Siguier, P.
Perochon, J.
Lestrade, L.
Mahillon, J.
Chandler, M.
ISfinder: the reference centre for bacterial insertion sequences
title ISfinder: the reference centre for bacterial insertion sequences
title_full ISfinder: the reference centre for bacterial insertion sequences
title_fullStr ISfinder: the reference centre for bacterial insertion sequences
title_full_unstemmed ISfinder: the reference centre for bacterial insertion sequences
title_short ISfinder: the reference centre for bacterial insertion sequences
title_sort isfinder: the reference centre for bacterial insertion sequences
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347377/
https://www.ncbi.nlm.nih.gov/pubmed/16381877
http://dx.doi.org/10.1093/nar/gkj014
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