New gene-finder for S.pombe and MONOCOTS

webmaster webmaster at mail.softberry.com
Wed Nov 1 10:09:31 EST 2000


New gene-finder sets of  S.pombe and Monocot plants 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


   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 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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