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| | Plant Repeat Database Project |
| TIGR | TIGR Database | TIGR Plant Genomics | Project Home | Introduction | | ||
Methods to Create the TIGR Plant Repeat DatabasesRepetitive DNA sequences of selected plant genera were queried from GenBank and other published records. After eliminating the duplicated sequences and vector sequences, the repeats were coded into five superclasses: Transposable elements, Centromere-related, Telomere-related, rDNA and Unclassified. The superclasses were then broken down into major classes of repeats. The collected repetitive sequences within the same plant family were combined into a repeat database for the plant family.
The TIGR-extracted repeats for a genus (e.g. Oryza), if available, were generated by searching available genomic sequences from the HTGS and PLN divisions of GenBank with the family repeat database (e.g. TIGR Gramineae Repeat Database) using FLAST. Genomic sequences that matched a repetitive DNA sequence in the family repeat database with ~75% identity and ~95% in overall length were selected, and coded accordingly. The sequences were combined with repetitive sequences obtained previously from public databases, to create the TIGR Repeat Database for that genus. Please click here to get the composition of each repeat database.
For Comments/Questions send mail to The TIGR plant repeat database team.
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