BLAT-based comparative analysis for transposable elements: BLATCAT.

Biomed Res Int 2014 18;2014:730814. Epub 2014 May 18.

Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea ; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea.

The availability of several whole genome sequences makes comparative analyses possible. In primate genomes, the priority of transposable elements (TEs) is significantly increased because they account for ~45% of the primate genomes, they can regulate the gene expression level, and they are associated with genomic fluidity in their host genomes. Here, we developed the BLAST-like alignment tool (BLAT) based comparative analysis for transposable elements (BLATCAT) program. The BLATCAT program can compare specific regions of six representative primate genome sequences (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) on the basis of BLAT and simultaneously carry out RepeatMasker and/or Censor functions, which are widely used Windows-based web-server functions to detect TEs. All results can be stored as a HTML file for manual inspection of a specific locus. BLATCAT will be very convenient and efficient for comparative analyses of TEs in various primate genomes.

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Source
http://www.hindawi.com/journals/bmri/2014/730814/
Publisher Site
http://dx.doi.org/10.1155/2014/730814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4052159PMC
February 2015
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