Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    COTRASIF: conservation-aided transcription factor binding site finder

    20th May 2008

    With this post, I’m finally announcing the opening of the (mostly) functional COTRASIF web-tool, created for the genome-wide identification of promoter regulatory sequences (transcription factor binding sits, TFBS). You can learn more from the About and Help pages. For an example of use, see the Supplement page (article is currently being prepared; as soon as it’s ready, I’ll make it available).

    If you are interested – have a look at the News page, where there is information on joining COTRASIF Google group. For non-public enquiries, please use my contact page.

    Note: the problem of identifying eukaryotic transcription factor binding sites stays acute for many years in a row – see e.g. the most recent Eukaryotic transcription factor binding sites – modelling and integrative search methods.

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    6 Responses to “COTRASIF: conservation-aided transcription factor binding site finder”

    1. BGRS-2008 conference in Novosibirsk, Russia » Autarchy of the Private Cave Says:

      [...] some work in genomics (namely, our COTRASIF tool) [...]

    2. Grumo Says:

      TATAGGTTGTTTTAATTGGAAGCAAACCCAGTTTCATTACCTCAAGCAAATTTCTTCATCTCTTTTAGCTTCCGT
      TTCTCATCTCTTTTTTTTTTTTGAGATAGAGTCTTGCTCTGTCGCACAGGCTGGGTTGGGTGCAGTGGTGCGATC
      TTGGCTCACCGCAACCTCTGCCTCCCAGGTTCAAGCAATTCTTCTGCCTCAGCCTCCTGAATAGCTGGGACTACA
      GGCGCCTGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGATGGC
      CTCCATCTCCTGACTCCGTGATCCACCCGCCTCGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACCGCGC
      CCGGCAGTCCGTTTCTCATCTTTAAAGTGAGAGTGCTAACACGCACATGGAGGGCTACTATGAGAATGGAGTGAG
      ATTTTGTATATGAAGTAGCAAAGACAGAGCCTGGGACTTAGTAGGTACATTATTAAGAGTTGGAGCCATTTTTTA
      AACCTTTTGTCTTTTTGTTATTTTTGCTGTTCTGAAAGTCTCTAAGCTTTTAAAAATGGTCTCTTATTTTACTAT
      TCTTGAATTGTTTCACGCTTCTCAACTCATGACAAGAACCTATTCTGCCAATGAACCTCCTGCCCCCATCTATTG
      AAATTAAAGCTTAGGAGCACCAGTGCATCCCAGAATTTGACTTCCTTCCAGTGGAGAGACCCCTTGGGTTTTTCG
      TGTGCTCTTTCCCTGATCCTTTAGGTGTCACATGGTCAGAAAGAACATAGTATTATTTATAAACAATATGCTCTC
      TAACTTCAGAAAGATTTAGGACAGCTTTCTGGATTTGGTCATGCATGAAACAGGAAAAACAGGCTATTAGAAAAT
      TGTGTGAAGTCTAACAGGGACTTGATATGAATTCATTTTGATTTTTAAAACTGAGGACTGCAATCATTAATCAGT
      TCATTAAATTAATTGGAATAAGTATATTGCATGTAGTGAGAGTAGTAGTATTTTTTGAAATTTTAGTTTTAATTA
      TATCCTATGGCCTGTGTTGTAAGATTTTTTATTTTAAGAGTTTAAAAGCCATTCGATTAAGCAACTAGTAGTAAA
      CTTTTCTGTCTCTCATTAGTTGTTAAATCTAGAAAAGTTATTGGTTTAACAAACCTTTATTGGATATCTATTTTG
      CATCAGATTTTTTTCTACATGAATGACATTTTTTTCTCTCTCTTTTCTAATACTGATTTGTTGCAGTGTCGAATA
      GGTACCTGGGTCAACTCCACACACTTCTCACTCTTCACTGGACCTCTGGTACAAGATTGAGAGGATTCCTATTAC
      TTACAAACAGACTAGGTATTAAAACAAAAAGATTCCCGAATAGAGTGAACCTAACCTAGAGCCCCTAAGAATTAC
      ATCAGCTTTAACCATTAATTCCCTGGGTTCTTCTTATTCAGTAATGTCTTAAAACCTTTTTATCAGTATGGGATG
      GGCGGGCAAGGGGATAAAGAAACTGGCGGCTGGTGGGAAGCCTTAGGTAAGGCTGTCAGGGGGGCTTTAGTTTGG
      GAGTGGGATAATTTGCTGAGGAAGGGTGGGAGAAACGTGAACTAGCACACAAAAGGCTGTTTCCGGCTCAAATTT
      CGTTACCAAGGCTCTTTGAGATGAACTTTTTTGGGGGAAAACAATCAGTCTAAAAGAGCTGTGTCTTCTTGTGTG
      TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACAAGGGGGCGGCGAGGGTCCCCACTTTTAGTATGAGTAGCA
      TTGTTCACATGTTTGCCAGTATTTTGGAGCCTGGCAGGCCTGGGTAGAGGCTGCGGGGGACGCCTCCAAGTTCCC
      ACCCGGGACATCCTGAACAGCAGCAGCCACAACAACAGGCTCGCCCCTAGACAAAGGGGCCGGCGCGGCGGAGCA
      GACTGGTGCAGCCTGGGCCGCGCGCTCAGAGCGCTGGGCGTCTGGGCAGCTGAGTGGGCAGAGCTGACCCGGTGC
      GGGTGGGAGTCAGGGCGCCCGGAAAACCCGGCTCTGGGTAGCAGACCCCGCCCGGGCTGGCTCGGCGCCGGGCCT
      TCGGGCTTCCACTCAGTCTTTGACCCTCGGTCCTCGCTCAGCGGCCCGGCAGGCCGCACAACTGTAACCGCTGCC
      CCGGCCGCCGCCCGCTCCTTCTCGGTCCGGCGGGCACAGAGCGCAGCGCGGCGGGGCCGGCGGC

    3. Bogdan Says:

      Comment form doesn’t do anything, please use proper address.

      Also, using custom promoters is not supported – only internal database of promoters is searched. If you prefer to work with your sequences, please download standalone version.

    4. Mehdi Says:

      >readseq-5371_tmp_1 101 bp
      CGTCTGGAAGACACAGGCAGATAGCGCTCGCCTCAGTTTCTCCCACCCCCACAGCTCTGC
      TCCTCCACCCACCCAGGGGGCGGGGCCAGAGGTCAAGGCTA

    5. Bogdan Says:

      Comment form doesn’t do anything, please use proper address.

      Also, using custom promoters is not supported – only internal database of promoters is searched. If you prefer to work with your sequences, please download standalone version.

    6. The 9th ICSB-2008 in Gothenburg, Sweden Says:

      [...] there was some interest in the tool I presented – the COTRASIF. Although it is not strictly systems-biology (actually, it is pure genomics tool), there were [...]

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