Title |
VennBLAST—Whole transcriptome comparison and visualization tool
|
---|---|
Published in |
Genomics, December 2014
|
DOI | 10.1016/j.ygeno.2014.12.004 |
Pubmed ID | |
Authors |
Tamar Zahavi, Gil Stelzer, Lior Strauss, Asher Y. Salmon, Mali Salmon-Divon |
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 merits 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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | 13% |
Netherlands | 2 | 8% |
France | 1 | 4% |
Taiwan | 1 | 4% |
Sweden | 1 | 4% |
Spain | 1 | 4% |
Israel | 1 | 4% |
Finland | 1 | 4% |
United Kingdom | 1 | 4% |
Other | 5 | 21% |
Unknown | 7 | 29% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 13 | 54% |
Members of the public | 11 | 46% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | 2% |
Chile | 1 | <1% |
Uruguay | 1 | <1% |
Brazil | 1 | <1% |
Germany | 1 | <1% |
Slovakia | 1 | <1% |
United Kingdom | 1 | <1% |
Japan | 1 | <1% |
Argentina | 1 | <1% |
Other | 0 | 0% |
Unknown | 113 | 91% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 34 | 27% |
Student > Ph. D. Student | 27 | 22% |
Student > Master | 10 | 8% |
Student > Bachelor | 9 | 7% |
Student > Doctoral Student | 7 | 6% |
Other | 18 | 15% |
Unknown | 19 | 15% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 60 | 48% |
Biochemistry, Genetics and Molecular Biology | 19 | 15% |
Environmental Science | 5 | 4% |
Computer Science | 4 | 3% |
Medicine and Dentistry | 3 | 2% |
Other | 12 | 10% |
Unknown | 21 | 17% |