Interspecific Comparative Clustering and Annotation foR Est

  • Iccare Abstract
  • Iccare Documentation
  • Iccare Resources
  • Cited References

  • Iccare Abstract

    The Iccare Web server, http://bioinfo.genopole-toulouse.prd.fr/iccare, provides a simple yet efficient tool for crude EST annotation specifically dedicated to comparative mapping approaches. Iccare uses all the EST and mRNA sequences of public databases for an organism of interest (query species) and compares them to all the transcripts of one reference organism (Homo sapiens or Arabidopsis thaliana). The results are displayed according to the location of the genes on the chromosomes of the reference organism. Gene structure information and sequence similarities are combined in a graphical representation in order to pinpoint the nature of the transcript query sequence. The user can subsequently design primers or probes for the purpose of physical or genetic mapping. In addition to the query organisms already available in Iccare, users can perform a tailor-made search with their own sequences against the animal or plant reference organism genes.

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    Iccare Documentation

    Software desciption

    All the sequences are screened for vectors and masked for known repeats with RepeatMasker [UniVec at ftp://ftp.ncbi.nih.gov/pub/UniVec, Smit A & Green P, RepeatMasker at http://ftp.genome.washington.edu/RM/RepeatMasker.html]. The masked sequences are subsequently compared to all the transcript sequences of the reference organism with the blastn option of the BLAST program [1]. The results are filtered according to the expected value. This value is normalized in order to fit a standardized e-value of a comparison with a database of 1 million residues. Only similarities, or more precisely, using the terminology of BLAST, Highest Scoring Pair (HSP) with an expected value less than 10-5 are kept for further consideration (the complete blast output is also available). Finally, Iccare compiles the BLAST results, the mapping information of the reference organism and formats these results for the web site application.

    Web Site Dynamic Script

    Programming was done in Perl using the CGI library, the GD library and the EMBOSS package [2].

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    Iccare Resources

  • Model and query organisms sequences and information
  •   NCBI  
      Human UniGene transcript sequences.  
      Human mapping gene information.  
      MAtDB Arabidopsis cDNA sequences.  
      Query organisms ESTs / mRNA sequences.  

  • Tools
  • Primer3 Primer Design.
    OverGo Maker Overgo probes Design (by OverGo Maker 40).

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    Cited References

    1. Altschul S.F., Madden T.L., Schaeffer A.A., Zhang J., Miller W. and Lipman D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.

    2. Rice P., Longden I. and Bleeasby A. (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics, 16(6), 276-277.

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    © Iccare : Laboratoire de génétique cellulaire - INRA &
    Laboratoire de Biotechnologies et d'Amélioration des Plantes - INP-ENSAT.
    Created by Faraut & Muller 02/2003 .