New Plasmodium falciparum finding Genes

[Victor]

      New Plasmodium falciparum finding Genes
parameters for FGENESH

              the program with parameters for major
model organisms
                    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 +

KFASKKNNQKNSSKNDERYRELDNLVQEGNGSRLGGGSCLGKCAHVFKLIFKEIKDNIF

YILSIIYLSVCVMNKIFAKRTLNKIGNYSFVTSETHNFICMIMFFIVYSLFGNKKGNSK

RHRSFNLQFFAISMLDACSVILAFIGLTRTTGNIQSFVLQLSIPINMFFCFLILRYRYH

LYNYLGAVIIVVTIALVEMKLSFETQEENSIIFNLVLISALIPVCFSNMTREIVFKKYKI

DILRLNAMVSFFQLFTSCLILPVYTLPFLKQLHLPYNEIWTNIKNGFACLFLGRNTVVEN

CGLGMAKLCDDCDGAWKTFALFSFFNICDNLITSYIIDKFSTMTYTIVSCIQGPAIAIAY

YFKFLAGDVVREPRLLDFVTLFGYLFGSIIYRVGNIILERKKMRNEENEDSEGELTNVDS
 IITQ
 
 --- 

=====



Moderated
bionet.genome.gene-structure



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