TOOLS FOR PREDICTION AND ANALYSIS OF PROTEIN-CODING GENE STRUCTURE
Revealing of repeated elements
Prediction of repeated elements in newly sequenced DNA becomes very important in large genome sequencing projects, since precense of repeats in a query sequence can create a lot of problems for homology searches. The problem is complicated due to high heterogeneity and short length of repeated elements.
Homology searches against the collection of repeated element (Jurka J, Walichiewicz J and Milosavljevic A J (1992) Prototypic sequences for human repetitive DNA. J. Mol. Evol. 35, 286-291) are used for repeats revealing. We implemented a program for that purpose called REPEAT. Results of REPEAT are using in the ESTMAP and GenEdit systems for ESTs mapping, although output information about repeats is much more brief in ESTMAP and GenEdit. Censored sequence (with 'N's instead of repeated elements) is produced by the REPEAT program. If you need more details about repeated elements (alignments etc.), please, use the CENSOR server (one can obtain more information by sending a word "help" to firstname.lastname@example.org).
Milanesi L. and Rogozin I.B. Prediction of human gene structure. In: Guide to Human Genome Computing (2nd ed.) (Ed. M.J.Bishop) Academic Press, Cambridge, 1998, 215-259.
Milanesi L., D'Angelo D., Rogozin I.B. GeneBuilder: interactive in silico prediction of genes structure. Bioinformatics, 1999, (in press - BIO98N149).