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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.

This entry was posted on Tuesday, May 20th, 2008 at 19:33 and is filed under Bioinformatics, Links, Science, Software, Web. You can follow any responses to this entry through the RSS 2.0 feed. You can skip to the end and leave a response. Pinging is currently not allowed.

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

1. BGRS-2008 conference in Novosibirsk, Russia » Autarchy of the Private Cave Says:
   July 10th, 2008 at 1:57

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

2. Grumo Says:
   September 2nd, 2009 at 12:15

   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:
   September 2nd, 2009 at 12:36

   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:
   April 13th, 2010 at 13:23

   >readseq-5371_tmp_1 101 bp
   CGTCTGGAAGACACAGGCAGATAGCGCTCGCCTCAGTTTCTCCCACCCCCACAGCTCTGC
   TCCTCCACCCACCCAGGGGGCGGGGCCAGAGGTCAAGGCTA

5. Bogdan Says:
   April 13th, 2010 at 16:02

   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:
   June 8th, 2010 at 7:23

   [...] 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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