New gene-finder for MONOCOTS (Rice, Corn, Wheat) and for S.pombe

Softberry, Inc webmaster at mail.softberry.com
Tue Oct 31 21:01:48 EST 2000


New gene-finder for MONOCOTS and S.pombe parameters specific for 
MONOCOTS (Rice, Corn, Wheat) and for Schizosaccharomyces pombe are 
developed for FGENESH HMM based multiple gene prediction in genomic 
DNA

It is available for public at WEB server:

  http://www.softberry.com/gf/gf.html


FGENESH with Monocots specific parameters has gene-prediction accuracy about
10% higher in Monocot genomic DNA, than using Arabidopsis parameters.

TO USE a specific version check organism button, FGENESH button and click
Perform searh


    Post your sequence to the window or load your file with sequence in FASTA
format

Example of an output of the program for 145312 based of Oryza sativa 
genomic DNA:

  fgenesh  Tue Oct 31 14:55:37 EST 2000
  FGENESH 1.c Prediction of potential genes in Plant(Mct) genomic DNA
  Time:   Tue Oct 31 14:55:37 2000
  Seq name: gi|11034690|dbj|AP002855.2|AP002855 Oryza sativa genomic 
DNA, chromosome
1, BAC clone:OSJNBa0086P08
  Length of sequence:  145312  GC content: 45 Zone: 1
  Number of predicted genes 19 in +chain 9 in -chain 10
  Number of predicted exons 86 in +chain 44 in -chain 42
  Positions of predicted genes and exons:
   G Str Feature    Start     End   Score        ORF           Len

   1 -     PolA      76             -4.56
   1 -   1 CDSl     235 -     361    2.04     235 -     360    126
   1 -   2 CDSi     764 -    1014    0.13     766 -    1014    249
   1 -   3 CDSi    1100 -    1219    1.17    1100 -    1219    120
   1 -   4 CDSi    1486 -    1721   19.04    1486 -    1719    234
   1 -   5 CDSi    3328 -    3433    2.42    3329 -    3433    105
   1 -   6 CDSi    4854 -    5008    4.32    4854 -    5006    153
   1 -   7 CDSf    5906 -    6311    7.68    5907 -    6311    405
   1 -     TSS     6336             -3.59

   2 -     PolA   12166              0.44
   2 -   1 CDSl   12405 -   12568    9.35   12405 -   12566    162
   2 -   2 CDSi   12723 -   12926   13.54   12724 -   12924    201
   2 -   3 CDSi   14961 -   15165    5.65   14962 -   15165    204
   2 -   4 CDSi   15442 -   15588   22.87   15442 -   15588    147
   2 -   5 CDSf   15927 -   16121   13.31   15927 -   16121    195
   2 -     TSS    17206             -4.19
.............................................................
Predicted protein(s):
>FGENESH   1   7 exon (s)    235  -   6311    466 aa, chain -
MWAPHVILSLSSSSPLPSLFLSPSPLRPSVRSERRRAGAEVTATVAGPDAGASWSGGGDG
CGPEWWRPAGAEAADGGGGRLELTRVEGRRRRRRHWTTRSHLLAAAMRMDAGRWWTATRS
SDPGIGSGGGGGGEGASSYCSRGPLKKSIPSKQRIMFGVVVTDALLEWSAAVHFGVLRKL
PKGKGGECGISAGLMDYFVITTPNFVLDHEETISQNVGGQVHGVVLIAVGKLRVVTIRSA
HSGVSNVSVETPPDNEASVTGAAYGFRGATTSLTNEMLTLSKKITLVRHGLSTWNAESRV
QGSSNLSVLTETGAKQAEKCRDALANMKFDVCFSSPISRAKSTAEIIWKGKEEPLIFLDS
LKEAHLFFLEGMTNGMLLLVQAFNLFTLTVHLRKMTLVNTWRQRMLRRNIQSCTPDGGRI
LQISRFRSIDVNNGGMCVFTVNKRGEAMLQALNMTAHMYSDHTYQY
>FGENESH   2   5 exon (s)  12405  -  16121    304 aa, chain -
MASSRILVIGGTGRLGRHLVTASLDAGHPTAVLVRRPATAGARADSPVKAKLTEELCDNG
ARLVYGDVNDHDILVAAIKNADVVICAVGHTTPHKLVENQIKIMEAIRDAGNVKLAEQML
EPARSILGAKLRVREALRASGIPHTIVCGYLVHGFLLPKAGNPEADGPPVTTATIFGDGK
QKAMFVDDKDMSAVTIKAEEDPRTVDKILYVQPPANLCSLNQLVSVLEKKIGRDLEKCYV
PEEELAIKIEAASPFPLNFQLAIVHSALLPGVASCGQTAVRVEATELYPDMEYVTVEEYF
DSLI
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