Search our Database of Scientific Publications and Authors

I’m looking for a

    Details and Download Full Text PDF:
    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.
    PDF Download - Full Text Link
    ( Please be advised that this article is hosted on an external website not affiliated with
    Source Status ListingPossible

    Similar Publications

    Analysis of transposable element sequences using CENSOR and RepeatMasker.
    Methods Mol Biol 2009 ;537:323-36
    School of Biology, Georgia Institute of Technology, Atlanta, GA, USA.
    Eukaryotic genomes are full of repetitive DNA, transposable elements (TEs) in particular, and accordingly there are a number of computational methods that can be used to identify TEs from genomic sequences. We present here a survey of two of the most readily available and widely used bioinformatics applications for the detection, characterization, and analysis of TE sequences in eukaryotic genomes: CENSOR and RepeatMasker. For each program, information on availability, input, output, and the algorithmic methods used is provided. Read More
    Transposable element annotation of the rice genome.
    Bioinformatics 2004 Jan;20(2):155-60
    Department of Biology, McGill University, Montreal, Quebec, H3A 1B1 Canada.
    Motivation: The high content of repetitive sequences in the genomes of many higher eukaryotes renders the task of annotating them computationally intensive. Presently, the only widely accepted method of searching and annotating transposable elements (TEs) in large genomic sequences is the use of the RepeatMasker program, which identifies new copies of TEs by pairwise sequence comparisons with a library of known TEs. Profile hidden Markov models (HMMs) have been used successfully in discovering distant homologs of known proteins in large protein databases, but this approach has only rarely been applied to known model TE families in genomic DNA. Read More
    Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes.
    Chromosome Res 2011 Aug;19(6):787-808
    Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON L5L1C6, Canada.
    A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Read More
    Identification of human-specific AluS elements through comparative genomics.
    Gene 2015 Jan 7;555(2):208-16. Epub 2014 Nov 7.
    Department of Nanobiomedical Science & 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. Electronic address:
    Mobile elements are responsible for ~45% of the human genome. Among them is the Alu element, accounting for 10% of the human genome (>1.1million copies). Read More