Title

Authors

Affiliation

Department of Biology, Indiana State University, 200 North Seventh Street, Terre Haute, IN 47809, U.S.A

Email

Yongsheng.Bai@indstate.edu; *Corresponding author

Article Type

Software

Date

Received August 07, 2014; Accepted August 08, 2014; Published August 30, 2014

The schema for UCSC Known Genes (knownGene.txt) has been widely adopted for use in both standard and custom downstream analysis tools/scripts. For many popular model organisms (e.g. Arabidopsis), sequence and annotation data tables (including “knownGene.txt”) have not yet been made available to the public. Therefore, it is of interest to describe Tbl2KnownGene, a .tbl file parser that can process the contents of a NCBI .tbl file and produce a UCSC Known Genes annotation feature table. The algorithm is tested with chromosome datasets from Arabidopsis genome (TAIR10). The Tbl2KnownGene parser finds utility for data with other organisms having similar .tbl annotations.

Availability

Perl scripts and required input files are available on the web at http://thoth.indstate.edu/~ybai2/Tb12KnownGene

Citation

Bai, Bioinformation 10(8): 544-547 (2014)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.