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

Research output: Contribution to journal › Article › 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.

Original language	English
Pages (from-to)	497-499
Number of pages	3
Journal	Bioinformatics
Volume	22
Issue number	4
DOIs	https://doi.org/10.1093/bioinformatics/bti754
Publication status	Published - 15 Feb 2006
Externally published	Yes

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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.",

year = "2006",

month = feb,

day = "15",

doi = "10.1093/bioinformatics/bti754",

language = "English",

volume = "22",

pages = "497--499",

journal = "Bioinformatics",

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T2 - A tool for genome-wide search of coding and non-coding conserved sequence tags

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.

UR - https://www.scopus.com/pages/publications/32544431587

U2 - 10.1093/bioinformatics/bti754

DO - 10.1093/bioinformatics/bti754

M3 - Article

SN - 1367-4803

VL - 22

SP - 497

EP - 499

JO - Bioinformatics

JF - Bioinformatics

IS - 4

ER -

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

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