Plant and Nematode HMM GeneFinders (FGENESH)

Victor Solovyev solovyev at sanger.ac.uk
Wed Aug 4 20:12:58 EST 1999


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

  (in addition to HUMAN AND DROSOPHILA gene predictors)

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


Accuracy of the program is about 90% at the nucleotide level
to predict coding exons (AC = 0.5 (Sn + Sp)).

TO USE  specific version click Plant or Nematode 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  Mon Jul 12 16:28:07 BST 1999
 FGENESH 1.0 Prediction of potential genes in Plant(Dct) genomic DNA
 Time:   Mon Jul 12 16:28:07 1999
 Seq name: CGG WEB SERVER PAST Sequence
 Length of sequence:  4253  GC content: 37 Zone: 1
 Number of predicted genes 1 in +chain 1 in -chain 0
 Number of predicted exons 3 in +chain 3 in -chain 0
 Positions of predicted genes and exons:
  G Str Feature    Start     End   Score        ORF           Len

  1 +     TSS       15               -3.75
  1 +   1 CDSf    1681 -    1984     42.43    1681 -    1983    303
  1 +   2 CDSi    2162 -    2634     63.01    2164 -    2634    471
  1 +   3 CDSl    2733 -    3584     99.84    2733 -    3584    852
  1 +     PolA    4001               -0.45

Predicted protein(s):
>FGENESH   1   3 exon (s)   1681  -   3584    542 aa, chain +
MAKKGKEVLNALDAAKTQMYHFTAIVIAGMGFFTDAYDLFSISLVTKLLGRIYYHVDSSK
KPGTLPPNVAAAVNGVAFCGTLAGQLFFGWLGDKLGRKKVYGITLMLMVLCSLGSGLSFG
HSANGVMATLCFFRFWLGFGIGGDYPLSATIMSEYANKKTRGAFIAAVFAMQGFGILAGG
IVSLIVSSTFDHAFKAPTYEVDPVGSTVPQADYVWRIVLMFGAIPALLTYYWRMKMPETA
RYTALVARNTKQAASDMSKVLQVDLIAEEEAQSNSNSSNPNFTFGLFTREFARRHGLHLL
GTTTTWFLLDIAYYSSNLFQKDIYTAIGWIPAAETMNAIHEVFTVSKAQTLIALCGTVPG
YWFTVAFIDILGRFFIQLMGFIFMTIFMFALAIPYDHWRHRENRIGFLIMYSLTMFFANF
GPNATTFVVPAEIFPARLRSTCHGISAASGKAGAIVGAFGFLYAAQSSDSEKTDAGYPPG
IGVRNSLLMLACVNFLGIVFTLLVPESKGKSLEEISREDEEQSGGDTVVEMTVANSGRKV
PV


-- 
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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