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Tbl2KnownGene |
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Please cite: Bai, Y. Tbl2KnownGene: A command-line program to convert NCBI .tbl to UCSC knownGene.txt data file. Bioinformation 10(9). 2014 |
- Tool Description Tbl2KnownGene is a command-line program that parses the contents of a NCBI .tbl annotation table and produces a UCSC Known Genes annotation table. Tbl2KnownGene is written in Perl.
- Input files: NCBI .tbl annotation files (NCBI_Chr1.tbl, NCBI_Chr2.tbl, NCBI_Chr3.tbl, NCBI_Chr4.tbl, and NCBI_Chr5.tbl)
- Output files: UCSC knownGene annotation files (NCBI_Chr1.tbl2knownGene.txt, NCBI_Chr2.tbl2knownGene.txt, NCBI_Chr3.tbl2knownGene.txt, NCBI_Chr4.tbl2knownGene.txt, and NCBI_Chr5.tbl2knownGene.txt).
- Instructions: Please run the following command line on Unix or Mac machines with Perl installed (v5.7 or later).
- About the author:
perl Tbl2KnownGene.pl inputfile1 inputfile2 inputfile3 inputfile4 inputfile5
(e.g. perl Tbl2KnownGene.pl NCBI_Chr1.tbl NCBI_Chr2.tbl NCBI_Chr3.tbl NCBI_Chr4.tbl NCBI_Chr5.tbl)
Dr. Yongsheng Bai received his Ph.D. in Quantitative Biology from The University of Texas at Arlington in 2007. Currently he is an Assistant Professor in Department of Biology at Indiana State University, Terre Haute, Indiana, USA.
Dr. Bai has more than 10 years experience in bioinformatics and published his research work in many scientific journals and conferences. His current research interests lie in the development and refinement of bioinformatics algorithms/software and databases on NGS data, development of statistical model for solving biological problems, bioinformatics analysis of clinical data, as well as other topics including, but not limited to, large-scale genome annotation and comparative omics.