The PARIGA server for real time filtering and analysis of reciprocal BLAST results.

BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed...

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Autores principales:	Massimiliano Orsini, Simone Carcangiu, Gianmauro Cuccuru, Paolo Uva, Anna Tramontano
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b620715ec52b40d08636d0b0374e8da3
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spelling	oai:doaj.org-article:b620715ec52b40d08636d0b0374e8da32021-11-18T07:46:43ZThe PARIGA server for real time filtering and analysis of reciprocal BLAST results.1932-620310.1371/journal.pone.0062224https://doaj.org/article/b620715ec52b40d08636d0b0374e8da32013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23667459/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.Massimiliano OrsiniSimone CarcangiuGianmauro CuccuruPaolo UvaAnna TramontanoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e62224 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Massimiliano Orsini Simone Carcangiu Gianmauro Cuccuru Paolo Uva Anna Tramontano The PARIGA server for real time filtering and analysis of reciprocal BLAST results.
description	BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.
format	article
author	Massimiliano Orsini Simone Carcangiu Gianmauro Cuccuru Paolo Uva Anna Tramontano
author_facet	Massimiliano Orsini Simone Carcangiu Gianmauro Cuccuru Paolo Uva Anna Tramontano
author_sort	Massimiliano Orsini
title	The PARIGA server for real time filtering and analysis of reciprocal BLAST results.
title_short	The PARIGA server for real time filtering and analysis of reciprocal BLAST results.
title_full	The PARIGA server for real time filtering and analysis of reciprocal BLAST results.
title_fullStr	The PARIGA server for real time filtering and analysis of reciprocal BLAST results.
title_full_unstemmed	The PARIGA server for real time filtering and analysis of reciprocal BLAST results.
title_sort	pariga server for real time filtering and analysis of reciprocal blast results.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/b620715ec52b40d08636d0b0374e8da3
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The PARIGA server for real time filtering and analysis of reciprocal BLAST results.

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