NEW gene-finder FGENESH parameters for Neurospora crassa

webmaster webmaster at softberry.com
Wed Mar 14 11:08:26 EST 2001


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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