BLAT-Based Comparative Analysis for Transposable Elements : BLATCAT

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 associate...

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Bibliographic Details
Published in:BioMed research international 2014-01, Vol.2014 (2014), p.1-7
Main Authors: Lee, Sangbum, Oh, Sumin, Kang, Keunsoo, Han, Kyudong
Format: Article
Language:English
Subjects:
Algorithms
Animals
Comparative analysis
Computational Biology
Databases, Genetic
DNA Transposable Elements - genetics
Genetic research
Genome, Human
Genomes
Genomics
Humans
Java
Macaca mulatta
Methods
Monkeys & apes
Pan troglodytes
Primates
Primates - genetics
Sequence Alignment
Software
Transposons
User interface
Citations: Items that this one cites
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Summary: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.
ISSN:2314-6133
2314-6141
DOI:10.1155/2014/730814