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
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