BESTORF - Prediction of potential coding fragment in EST/mRNA sequence

Victor Solovyev solovyev at sanger.ac.uk
Tue Feb 23 15:50:42 EST 1999


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 (Mammalian) or Plant sequences (Arabidopsis)
(click Human 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     References: Solovyev V.V., Salamov A.A., unpublished data.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.

     Accuracy: Preliminary tests of mRNA and their fragments show that the
accuracy of recognition of true ORF is about 100% for typical
     mRNA and is about 99% for EST fragments 500 - 800 bp containing coding
region. It should be less if we will present EST with
     frameshift errors,

     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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