Using RepeatMasker to identify repetitive elements in genomic sequences

Current Protocols in Bioinformatics

Volumn , Issue SUPPL. 25, 2009, Pages

  Tarailo Graovac, Maja ^a   Chen, Nansheng ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Cross_match; Genome annotation; RECON; Repeat library; RepeatMasker; Repetitive elements; WU BLAST

Indexed keywords

BIOINFORMATICS; COMPUTER PROGRAM; COMPUTER SYSTEM; DNA SEQUENCE; DNA STRUCTURE; GENE LIBRARY; GENETIC ALGORITHM; INFORMATION PROCESSING; PRIORITY JOURNAL; REVIEW; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; WEB BROWSER;

GENOMICS; INTERNET; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 63049126614     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi0410s25     Document Type: Review

References (7)

1. Bao, Z. and Eddy, S.R. 2002. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12:1269-1276.
2. Bedell, J.A., Korf, I., and Gish, W. 2000. MaskerAid: A performance enhancement to RepeatMasker. Bioinformatics 16:1040-1041.
3. Jurka, J. 2001. Repbase update, a database and an electronic journal of repetitive elements. Trends Genet. 16:418-420.
4. Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., and Walichiewicz, J. 2005. Rep-base update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110:462-467.
5. Price, A.L., Jones, N.C., and Pevzner, P.A. 2005. De novo identification of repeat families in large genomes. Bioinformatics 21:SUppl 1:i351-358.
6. Smith, T.F. and Waterman, M.S. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147:195-197.
7. Stein, L.D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., Coulson, A., D'Eustachio, P., Fitch, D.H.A., Fulton, L., Fulton, R., Griffiths-Jones, S., Harris, T.W., Hillier, L.W., Kamath, R., Kuwabara, P.E., Marra, M., Mardis, E., Miner, T., Minx, P., Mullikin, J.C., Plumb, R.W., Rogers, J., Schein, J., Sohrmann, M., Spieth, J., Stajich, J.E., Wei, C., Willey, D., Wilson, R., Durbin, R., and Waterston, R. 2003. The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biol. 1:E45.