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

被引：3

作者：

Castrignanò, T

De Meo, PD

Grillo, G

Liuni, S

Mignone, F

Talamo, IG

Pesole, G ^{[1
]}

机构：

[1] CNR, Ist Tecnol Biomed, Sede Bari, I-70126 Bari, Italy

[2] Univ Ricerca, Consorzio Interuniv Appl Supercalcolo, CASPUR, Rome, Italy

[3] Univ Milan, Dipartimento Sci Biomol & Biotecnol, I-20133 Milan, Italy

来源：

BIOINFORMATICS | 2006年 / 22卷 / 04期

关键词：

D O I：

10.1093/bioinformatics/bti754

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：497 / 499

页数：3

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