Paper Info
Title
SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.
Abstract
The popularity of massively parallel exome and transcriptome sequencing projects demands new data mining tools with a comprehensive set of features to support a wide range of analysis tasks.SeqGene, a new data mining tool, supports mutation detection and annotation, dbSNP and 1000 Genome data integration, RNA-Seq expression quantification, mutation and coverage visualization, allele specific expression (ASE), differentially expressed genes (DEGs) identification, copy number variation (CNV) analysis, and gene expression quantitative trait loci (eQTLs) detection. We also developed novel methods for testing the association between SNP and expression and identifying genotype-controlled DEGs. We showed that the results generated from SeqGene compares favourably to other existing methods in our case studies.SeqGene is designed as a general-purpose software package. It supports both paired-end reads and single reads generated on most sequencing platforms; it runs on all major types of computers; it supports arbitrary genome assemblies for arbitrary organisms; and it scales well to support both large and small scale sequencing projects. The software homepage is http://seqgene.sourceforge.net.
Year
DOI
Venue
2011
10.1186/1471-2105-12-267
BMC Bioinformatics
Keywords
Field
DocType
bioinformatics,algorithms,copy number variation,data mining,data integrity,quantitative trait loci,microarrays,gene expression
Transcriptome Sequencing,Biology,Massively parallel,Exome,Software,Bioinformatics,Genetics
Journal
Volume
Issue
ISSN
12
1
1471-2105
Citations 
PageRank 
References 
12
0.51
13
Authors
1
Name
Order
Citations
PageRank
Xutao Deng1868.22