Paper Info
Title
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags.
Abstract
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.
Year
DOI
Venue
2006
10.1093/bioinformatics/bti754
Bioinformatics
Keywords
Field
DocType
conserved sequence tag,transcript sequence,user-specified whole genome assembly,gene finding,genome-wide search,genominer software,sequence region,suitable coding potential score,coding sequences,regulatory regions,vertebrate genome assembly,molecular evolution,query sequence,genome-wide similarity search,genome annotation,non-coding nature,user-submitted genome,similarity search
Genome,Software tool,Data mining,Conserved sequence,Computer science,Coding (social sciences),Blat,Software,Bioinformatics
Journal
Volume
Issue
ISSN
22
4
1367-4803
Citations 
PageRank 
References 
3
0.45
4
Authors
7
Name
Order
Citations
PageRank
Tiziana Castrignanò110310.37
Paolo D'onorio De Meo2848.28
Giorgio Grillo323755.68
Sabino Liuni437686.28
Flavio Mignone512812.90
Ivano Giuseppe Talamo6302.50
Graziano Pesole7942107.35