New Drosophila specific gene-finding HMM based program FGENESH

Victor Solovyev solovyev at sanger.ac.uk
Wed Mar 17 15:54:26 EST 1999


 We installed New Drosophila specific gene-finding HMM based program FGENESH
    for multiple gene prediction in  genomic DNA

It is available at http://genomic.sanger.ac.uk/ of our
Computational Genomic Group WEB server
(http://genomic.sanger.ac.uk/gf/gf.html)

For analysis of Drosophila DNA FGENES or FGENESH versions
  for human DNA can be used, however Drosophila
specific version has better exact exon prediction accuracy.

Accuracy of the program was estimated on a set of 500 sequences
containing one gene each (simple test)

It is about 94% at the nucleotide level and
            74% of exons can be predicted exactly

TO USE Drosophila specific version click Drosophila button + fgenesh button

TO USE Human specific version click Human button + fgenesh button

   Past your sequence to the window or load your file with sequence in FASTA
fromat

Example of output of the program:

 FGENESH 1.0 Prediction of potential genes in Drosophila genomic DNA
 Time:   Tue Mar 16 15:11:34 1999.
 Seq name: AB003910     4755 bp    DNA             INV
 Length of sequence:  4755  GC content: 44 Zone: 1
 Number of predicted genes 1 in +chain 1 in -chain 0
 Number of predicted exons 2 in +chain 2 in -chain 0
 Positions of predicted genes and exons:
  G Str Feature    Start     End   Score        ORF           Len

  1 +     TSS     2679             -6.30
  1 +   1 CDSf    2753 -    3677  227.30    2753 -    3676    924
  1 +   2 CDSl    3739 -    3944   41.75    3741 -    3944    204
  1 +     PolA    4312              1.05

Predicted protein(s):
>FGENESH   1   2 exon (s)   2753  -   3944    376 aa, chain +
MCDDDAGALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNSPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGFALPHAILRLD
LAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAAASTSLEKS
YELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETVYNSIMKCDVDIRKDLYANSVL
SGGTTMYPGIADRMQKEITALAPSTIKIKIIAPPERKYSVWIGGSILASLSTFQQMWISK
QEYDESGPGIVHRKCF

-- 
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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