RegScan System for DNA sequence analysis

Aim: RegScan system allows the specific contextual, conformational, and physico-chemical properties to be revealed basing on analysis of extended DNA regions.

Initially the system RegScan has been designed to analyze the extended regulatory regions of eukaryotic genes. The computer system comprises the following software:

  1. programs for classification dividing a set of promoters into TATA-containing and TATA-less promoters and promotes with and without CpG islands;
  2. programs for constructing (a) nucleotide frequency profiles, (b) sequence complexity profiles, and (c) profiles of conformational and physico-chemical properties;
  3. the program searching for and visualizing repeats in nucleotide sequences.
  4. the program for constructing sets of degenerate oligonucleotide motifs of a specified length.

Applicability: In the general case, this set of programs can be used for analyzing any genomic DNA sequences.

Source data: In (1), (4) units there should be a set of DNA sequences to provide some statistics on the features obtained. In (3) there should be a single DNA sequence as an input data.

Restrictions: DNA sequences should not exceed 32 kilobases.

Copyright: Institute of Cytolgy & Genetics, Novosibirsk, 630090, Russia

References:

  1. Babenko, V.N., Kosarev, P.S., Basin, V.G. Searching for the repeats in regulatory regions of eukaryotic genes. Proc. of International school of theoretical biophysics, Moscow, 1998, Russia, p.28.
  2. Kosarev, P.S., Babenko, V.N. Promoters: AT/GC content and properties of TATA - box. Proc. of I International Conference on Bioinformatics of Genome Regulation and Structure, 1998. Novosibirsk, Russia, pp.119-124.
  3. Kondrakhin, Yu. V., Babenko, V.N., Milanesi, L., Lavryushev, S.V., Schug, J., Kolchanov, N.A. Recognition groups: a new method for description and prediction of transcription factor binding sites. Bioinformatics, 1999, accepted
  4. Kel, A.E., Ptitsyn, A.A. Babenko, V.N., Meier - Ewert, S., Lehrach, H. A genetic algorithm for designing gene family specific oligonucleotide sets for hybridization: The G protein-coupled receptor protein superfamily. Bioinformatics, 1998, v. 14, N. 3, pp.259-270;
  5. Kolchanov, N.A., Vishnevsky, O.V., Babenko, V.N., Kel, A.E., Shindyalov, I.N. Identification of cDNA sequences by specific oligonucleotide sets. Computer tool and application. Proc. of 3-rd international conference on intelligent systems for molecular biology, London, 1995,pp.206-214.
  6. Vishnevsky, O.V., Podkolodnaya, O.A., Babenko, V.N. Search for degenerate oligonucleotide motifs in transcription factor binding sites and eukaryotic promoters (Computer system ARGO). Proc. of I International Conference on Bioinformatics of Genome Regulation and Structure, 1998, Novosibirsk, Russia, pp.144-146.
  7. Kolchanov, N.A., Babenko, V.N.,Vishnevsky, O.V., Kel, A.E. Oligonucleotide vocabularies of isofunctional gene families coding for proteins. Proceedings of Academy of Science (DAN). 1996, v.348, n5, pp.636-639 (in Russian).
  8. Kel., A.E., Philippenko, M.V., Babenko, V.N., Kolchanov, N.A. Genetic algorithm for selection of oligonucleotides for identification by hybridisation of genomic DNA fragments possessing gene potential. Proceedings of German Conference on Bioinformatics. Lepzig, 1996. pp.238-240.

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