title: SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Bioinformatics Core Facility, Department of Molecular Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA. xutaodeng@gmail.com
authors.forename: Xutao
authors.initials: X
authors.lastname: Deng
mesh_terms: D056915:DNA Copy Number Variations; D057225:Data Mining; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software