Anopheles gambiae Gene finding parameters

Softberry Team softberry at softberry.com
Tue Nov 5 16:33:34 EST 2002


       Anopheles gambiae Gene finding 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 Anopheles
 gambiae is developed
 for FGENESH program. Accuracy of prediction of
 Plasmodium falciparum protein
 coding genes is about 98% on the nucleotide level.
 
 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  Tue Nov  5 16:23:15 EST 2002
  FGENESH 1.1 Prediction of potential genes in
 Anopheles_gambiae genomic DNA
  Time    :   Tue Nov  5 16:23:16 2002
  Seq name: Softberry SERVER PAST Sequence
  Length of sequence: 1542
  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        249               -4.78
    1 +    1 CDSf       301 -       564    2.25      
 301 -       564    264
    1 +    2 CDSi       632 -      1011   15.80      
 632 -      1009    378
    1 +    3 CDSl      1097 -      1289    3.27     
 1098 -      1289    192
    1 +      PolA      1314                2.25
 
 Predicted protein(s):
 >FGENESH:   1   3 exon (s)    301  -   1289   278
 aa, chain +

KQVISLVLFGLFCGNAVVTNANGQNTTEGPSHSGRIVNGIPVNISNYKYALSMRFDGEF

ICGASIITYSHALTAAHCVYNYQFMSSRLTLYGGSTSASSGGVEFPVVRLLYHPSYNSYK

SNLSDYDVAILTVPANSFSGKPNMAPLALQTKELPADTRCFVVGWGKRADGENEQPSVNQ

LLYANMNIVSQSDCATMWANSEHRCPACKQSITSNMVCAQYGNSMDTCRGDSGGALVCGG
 RLTGVVSFALYCSGIWPSVFAKVTAPTIRNFIRYIAGI
 
 --- 

=====



Moderated
bionet.genome.gene-structure



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