SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

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. Conclusion: SeqGene is designed as a general-purpose software package. It supports both paired-end reads and single reads generated on most sequencing platforms; i...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Xutao Deng
• Keywords: Biometrics, BMCBI 2011, Data Mining Tools, Ethnic Tibetans, General Purpose Software