GenoMiner: A tool for genome-wide search of coding and non-coding conserved sequence tags

Tiziana Castrignanò; Paolo D.Onorio De Meo; Giorgio Grillo; Sabino Liuni; Flavio Mignone; Ivano Giuseppe Talamo; Graziano Pesole

doi:10.1093/bioinformatics/bti754

GenoMiner: A tool for genome-wide search of coding and non-coding conserved sequence tags

Tiziana Castrignanò, Paolo D.Onorio De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano Giuseppe Talamo, Graziano Pesole

Risultato della ricerca: Contributo su rivista › Articolo in rivista › peer review

Abstract

Summary: GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.

Lingua originale	Inglese
pagine (da-a)	497-499
Numero di pagine	3
Rivista	Bioinformatics
Volume	22
Numero di pubblicazione	4
DOI	https://doi.org/10.1093/bioinformatics/bti754
Stato di pubblicazione	Pubblicato - 15 feb 2006
Pubblicato esternamente	Sì

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10.1093/bioinformatics/bti754

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title = "GenoMiner: A tool for genome-wide search of coding and non-coding conserved sequence tags",

abstract = "Summary: GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.",

author = "Tiziana Castrignan{\`o} and {De Meo}, {Paolo D.Onorio} and Giorgio Grillo and Sabino Liuni and Flavio Mignone and Talamo, {Ivano Giuseppe} and Graziano Pesole",

note = "Funding Information: We thank David Horner for valuable comments on the manuscript. This work was supported by Fondo Italiano Ricerca di Base (FIRB) projects {\textquoteleft}Bioinformatica per la Genomica e la Protomica{\textquoteright} and {\textquoteleft}Laboratorio Italiano di Bioinformatica{\textquoteright}, MIUR Cluster C03/ 2000-CEGB, PON 2000–2006 Progetto BIG, D.D. 9/10/2002 n.1105 obiettivo 1, EU STREP project TRANSCODE and by AIRC.",

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doi = "10.1093/bioinformatics/bti754",

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AU - Castrignanò, Tiziana

AU - De Meo, Paolo D.Onorio

AU - Grillo, Giorgio

AU - Liuni, Sabino

AU - Mignone, Flavio

AU - Talamo, Ivano Giuseppe

AU - Pesole, Graziano

N1 - Funding Information: We thank David Horner for valuable comments on the manuscript. This work was supported by Fondo Italiano Ricerca di Base (FIRB) projects ‘Bioinformatica per la Genomica e la Protomica’ and ‘Laboratorio Italiano di Bioinformatica’, MIUR Cluster C03/ 2000-CEGB, PON 2000–2006 Progetto BIG, D.D. 9/10/2002 n.1105 obiettivo 1, EU STREP project TRANSCODE and by AIRC.

PY - 2006/2/15

Y1 - 2006/2/15

N2 - Summary: GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.

AB - Summary: GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.

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GenoMiner: A tool for genome-wide search of coding and non-coding conserved sequence tags

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