New gene-finder parameters for Neurospora crassa is developed for
FGENESH HMM based multiple gene prediction in genomic DNA
It is available at:
http://www.softberry.com/nucleo.html
FGENESH with N.crassa specific parameters has gene-prediction accuracy about
10% higher in Monocot genomic DNA, than using S.pombe or S.cerevisiae parameters.
TO USE a specific version check organism button, FGENESH button and click
Perform searh
Past your sequence to the window or load your file with sequence in FASTA
fromat
Example of an output of the program for 145312 based of N.crassa genomic DNA:
FGENESH 1.0 Prediction of potential genes in N.crassa genomic DNA
Time: Tue Mar 13 13:33:39 2001
Seq name: C6 zinc cluster protein fluffy, fl, FL [AF022648 ]
Length of sequence: 3711 GC content: 51 Zone: 1
Number of predicted genes 1 in +chain 1 in -chain 0
Number of predicted exons 5 in +chain 5 in -chain 0
Positions of predicted genes and exons:
G Str Feature Start End Score ORF Len
1 + TSS 429 -4.66
1 + 1 CDSf 501 - 560 2.98 501 - 560 60
1 + 2 CDSi 711 - 1810 21.36 711 - 1808 1098
1 + 3 CDSi 1871 - 1986 6.92 1872 - 1985 114
1 + 4 CDSi 2049 - 2280 2.97 2051 - 2278 228
1 + 5 CDSl 2341 - 3211 27.95 2342 - 3211 870
Predicted protein(s):
>FGENESH 1 5 exon (s) 501 - 3211 792 aa, chain +
MPRQHLTPNACLVCRKKRTKCDGQMPCRRCRSRGEECAYEDKKWRTKDHLRSEIERLRNE
QRQGHAVIRALINDEQDWESFLSRIRGDESPEAIADWIRSIRNLFEPLQAASSQSMGGLG
APPTLLSPSQATASESSQLHRAASFAGIGSYNFGQGRVPFDQSTPRSSFSSDLSPTTPFS
FREQADFIHAPQPMYPSSRRFSSSSLPSLPLRHSSQPLVPGIFNEPLPHTWTSITSDTQL
VQRLLSRFFSAPCSLLCFIPQSSFMKAFREGDSRYCSEALVNAILGKACKSYGTASNIVS
RMAFGDAFIGEAKRLLATEPNHTNLPSTQALAVLALAEISEGKDDEAWDLAWASVRAAIT
REQSFHVDQEFATARAVSYCGGFTLIHMLRLLTGRLDLNTSPFFMRLYQGSEETPEDEPQ
NRIERGFALHMQFLAELEHCPPLPRFVFEITTAVHTFASYNFSNAATAEELEDAYGKCLD
AYKRFEETFCLDMDTTPDLLFAQIWYHYCLLALLRPFVKSTASLRDSAMTTPRLRNDANP
SDICQRSSEAIIFLTSTYQTRFSLGNPPELLPHMLFAAVLYQVTLTPDPEHLSTIANDIK
PELSESPVMMPSQAAFGAHGNSNLVPPPPMPFNNHGSYFPQPLSPVLKLEVRQAAPRRES
SISLSSTFDSCGNRRPSDSFTSSTLTSHDASERESSTSDTQSDFLPFFTSEPADLVTIGS
LQLASMQHHGAVEATRLLRSLSTVKDLVGSTLDLETLAEALPFPMGDLNTAVLYTGLGLQ
RAPVEPMQVTGP
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