New Plasmodium falciparum finding Genes parameters for FGENESH

Victor victor at softberry.com
Thu Oct 31 09:32:55 EST 2002


      New Plasmodium falciparum finding Genes parameters for FGENESH

             the program with parameters for major model organisms,
               viruses and bacteria is available for on line usage at:

              http://www.softberry.com/berry.phtml?topic=gfind

  Method description:

A new parameter set for gene prediction Plasmodium falciparum is developed
for FGENESH program. Accuracy of prediction of Plasmodium falciparum protein
coding genes is about 98% on the nucleotide level. Exact exon prediction
accuracy
~80%.

The FGENESH algorithm is based on pattern recognition of different types of
signals and Markov chain models of coding regions. Optimal combination of
these features is then found by dynamic programming and a set of gene
models is constructed along given sequence.

FGENESH is the fastest and most accurate ab initio  gene prediction program
available.


  Fgenesh output:

fgenesh  Wed Oct 30 23:05:15 EST 2002
 FGENESH 1.1 Prediction of potential genes in Plasmodium genomic DNA
 Time    :   Wed Oct 30 23:05:15 2002
 Seq name: MAL7P1.27 chr7 chloroquine resistance transporter
 Length of sequence: 4095
 Number of predicted genes 1 in +chain 1 in -chain 0
 Number of predicted exons 13 in +chain 13 in -chain 0
 Positions of predicted genes and exons:
   G Str   Feature   Start        End    Score           ORF           Len

   1 +      TSS        130               -4.02
   1 +    1 CDSf       501 -       591   18.40       501 -       590     90
   1 +    2 CDSi       769 -      1037   15.02       771 -      1037    267
   1 +    3 CDSi      1217 -      1389   18.26      1217 -      1387    171
   1 +    4 CDSi      1562 -      1694   21.53      1563 -      1694    132
   1 +    5 CDSi      1848 -      1919   26.11      1848 -      1919     72
   1 +    6 CDSi      2043 -      2118   12.63      2043 -      2117     75
   1 +    7 CDSi      2215 -      2297   19.19      2217 -      2297     81
   1 +    8 CDSi      2425 -      2475   25.92      2425 -      2475     51
   1 +    9 CDSi      2613 -      2669   19.99      2613 -      2669     57
   1 +   10 CDSi      2818 -      2910   14.46      2818 -      2910     93
   1 +   11 CDSi      3104 -      3148   19.99      3104 -      3148     45
   1 +   12 CDSi      3295 -      3349   23.81      3295 -      3348     54
   1 +   13 CDSl      3519 -      3595    9.78      3521 -      3595     75
   1 +      PolA      3691                2.25

Predicted protein(s):
>FGENESH:   1  13 exon (s)    501  -   3595   424 aa, chain +
MKFASKKNNQKNSSKNDERYRELDNLVQEGNGSRLGGGSCLGKCAHVFKLIFKEIKDNIF
IYILSIIYLSVCVMNKIFAKRTLNKIGNYSFVTSETHNFICMIMFFIVYSLFGNKKGNSK
ERHRSFNLQFFAISMLDACSVILAFIGLTRTTGNIQSFVLQLSIPINMFFCFLILRYRYH
LYNYLGAVIIVVTIALVEMKLSFETQEENSIIFNLVLISALIPVCFSNMTREIVFKKYKI
DILRLNAMVSFFQLFTSCLILPVYTLPFLKQLHLPYNEIWTNIKNGFACLFLGRNTVVEN
CGLGMAKLCDDCDGAWKTFALFSFFNICDNLITSYIIDKFSTMTYTIVSCIQGPAIAIAY
YFKFLAGDVVREPRLLDFVTLFGYLFGSIIYRVGNIILERKKMRNEENEDSEGELTNVDS
IITQ

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