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 +
MKFASKKNNQKNSSKNDERYRELDNLVQEGNGSRLGGGSCLGKCAHVFKLIFKEIKDNIF
IYILSIIYLSVCVMNKIFAKRTLNKIGNYSFVTSETHNFICMIMFFIVYSLFGNKKGNSK
ERHRSFNLQFFAISMLDACSVILAFIGLTRTTGNIQSFVLQLSIPINMFFCFLILRYRYH
LYNYLGAVIIVVTIALVEMKLSFETQEENSIIFNLVLISALIPVCFSNMTREIVFKKYKI
DILRLNAMVSFFQLFTSCLILPVYTLPFLKQLHLPYNEIWTNIKNGFACLFLGRNTVVEN
CGLGMAKLCDDCDGAWKTFALFSFFNICDNLITSYIIDKFSTMTYTIVSCIQGPAIAIAY
YFKFLAGDVVREPRLLDFVTLFGYLFGSIIYRVGNIILERKKMRNEENEDSEGELTNVDS
IITQ
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