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VennBLAST—Whole transcriptome comparison and visualization tool

Author:
Zahavi, Tamar, Stelzer, Gil, Strauss, Lior, Salmon, Asher Y., Salmon-Divon, Mali
Source:
Genomics 2015 v.105 pp. 131-136
ISSN:
0888-7543
Subject:
computer software, genes, high-throughput nucleotide sequencing, transcriptome
Abstract:
RNA-seq is the method of choice for getting a primary list of genes for non-model organisms. Once this is achieved, one would proceed to annotate the newly discovered genes and consequently strive to position the organism in an evolutionary context. These kinds of studies involving high-throughput sequencing generate large amounts of data, whose analysis might be time consuming for the non-specialist user and merit computational skills.Here we describe VennBLAST, a set of high-performance utilities that combines fast parallelized BLAST filtering with a visualization tool for whole-transcriptomic alignment comparison using Venn diagrams. The software accurately illustrates simple set relationships between numbers of matching sequences and identifies transcriptome conservation among different organisms. The intuitive Venn diagram visualization allows researchers to easily select a desired subset of genes for further inspection, using the DAVID functional annotation tools, for instance, which enables investigators to understand biological meaning behind large lists of genes.
Agid:
5527230