Anopheles gambiae Gene finding parameters for FGENESH

Softberry Team softberry at softberry.com
Wed Nov 6 15:18:11 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 +
MKQVISLVLFGLFCGNAVVTNANGQNTTEGPSHSGRIVNGIPVNISNYKYALSMRFDGEF
ICGASIITYSHALTAAHCVYNYQFMSSRLTLYGGSTSASSGGVEFPVVRLLYHPSYNSYK
SNLSDYDVAILTVPANSFSGKPNMAPLALQTKELPADTRCFVVGWGKRADGENEQPSVNQ
LLYANMNIVSQSDCATMWANSEHRCPACKQSITSNMVCAQYGNSMDTCRGDSGGALVCGG
RLTGVVSFALYCSGIWPSVFAKVTAPTIRNFIRYIAGI

---




More information about the Parasite mailing list