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Nucleic Acids Research 2005 33(Web Server Issue):W567-W569; doi:10.1093/nar/gki388
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© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

FeatureExtract—extraction of sequence annotation made easy

Rasmus Wernersson*

Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark Building 208, DK-2800 Lyngby, Denmark

*Tel: +45 452 52489; Email: raz{at}cbs.dtu.dk

Received February 14, 2005. Revised March 10, 2005. Accepted March 10, 2005.

Work on a large number of biological problems benefits tremendously from having an easy way to access the annotation of DNA sequence features, such as intron/exon structure, the contents of promoter regions and the location of other genes in upsteam and downstream regions. For example, taking the placement of introns within a gene into account can help in a phylogenetic analysis of homologous genes. Designing experiments for investigating UTR regions using PCR or DNA microarrays require knowledge of known elements in UTR regions and the positions and strandness of other genes nearby on the chromosome. A wealth of such information is already known and documented in databases such as GenBank and the NCBI Human Genome builds. However, it usually requires significant bioinformatics skills and intimate knowledge of the data format to access this information. Presented here is a highly flexible and easy-to-use tool for extracting feature annotation from GenBank entries. The tool is also useful for extracting datasets corresponding to a particular feature (e.g. promoters). Most importantly, the output data format is highly consistent, easy to handle for the user and easy to parse computationally. The FeatureExtract web server is freely available for both academic and commercial use at http://www.cbs.dtu.dk/services/FeatureExtract/.


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