BESTORF: Drosophila CDS recognition is installed in addition to Human and Plant CDS recognition

Victor Solovyev solovyev at sanger.ac.uk
Wed Aug 18 17:18:38 EST 1999


   Drosophila CDS recognition is installed in addition to Human and Plant CDS

BESTORF - Prediction of potential coding fragment in EST/mRNA sequence
===============================================================
it is available at http://genomic.sanger.ac.uk/ of our
Computational Genomic Group WEB server
(http://genomic.sanger.ac.uk/gf/gf.html)


Program prepared to analyze Human, Drosophila or Plant sequences (Arabidopsis)
 (click Human, Drosophila or Plant button, respectively)

     References: Solovyev V.V., Salamov A.A., unpublished data.


     Method description:
         Algorithm is based on Markov chain model of coding regions and a
probabilistic model to combine it with Start codon potential.


     The program output potential CDS positions (where the Start codon is
probable) as well as the longest ORF positions (as an extention of
     this CDS before the start codon). If observed Met codons are recognized as
internal, the CDS and ORF will have the same positions).


     BESTORF  Prediction of potential coding fragment in plant EST/mRNA
sequence
      Time:   Tue Feb 16 20:03:57 1999.
      Seq name: Seq_name:
      Length of sequence:  388
      Predicted CDS 1 in +chain 1 in -chain 0
      Position of predicted CDS/ORF:
       G Str Feature   Start      End   Score       ORF       CDS-Len Frame

       1 +   1 CDSo      30 -     386   30.57      3 -    386    357     +3

     Predicted protein fragment:
     >BESTORF   1   1 fragment (s)     30  -    386    119 aa, chain +
     MDELDILIVGGYWGKGSRGGMMSHFLCAVAEKPPPGEKPSVFHTLSRVGSGCTMKELYDL
     GLKLAKYWKPFHRKAPPSSILCGTEKPEVYIEPCNSVIVQIKAAEIVPSDMYKTGCTLR


-- 
Victor Solovyev
The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
Email: solovyev at sanger.ac.uk  http://genomic.sanger.ac.uk
Phone: 44-1223-494799  FAX:   44-1223-494919




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