NEW gene-finder FGENESH parameters for

webmaster webmaster at softberry.com
Mon Jun 4 21:51:16 EST 2001


NEW gene-finder FGENESH parameters for MOUSE genes

New gene-finder parameters for Mouse is developed
for 
FGENESH HMM based multiple gene prediction in
genomic DNA 
 Mouse specific parameters provide better accuracy
 than using Human parameters.
 
 It is available at: 
 
 http://www.softberry.com/nucleo.html 
 
 
 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 Mouse
 genomic DNA,
 where fgenesh predicted exactly ALL 30 exons: 
 
 fgenesh  Mon Jun  4 22:41:38 EDT 2001
  FGENESH 1.1 Prediction of potential genes in Mouse
 genomic DNA
  Time    :   Mon Jun  4 22:41:38 2001
  Seq name: BAT2, intron-exon boundaries defined in
 relation to human cDNA in M33509. Alt [AF109719 ] 
  Length of sequence: 14123 
  Number of predicted genes 1 in +chain 1 in -chain 0
  Number of predicted exons 30 in +chain 30 in -chain
 0
  Positions of predicted genes and exons:
    G Str   Feature   Start        End    Score      
     ORF           Len
 
    1 +    1 CDSf       201 -       312   11.96      
 201 -       311    111
    1 +    2 CDSi       805 -       982   10.66      
 807 -       980    174
    1 +    3 CDSi      1275 -      1374    6.44     
 1276 -      1374     99
    1 +    4 CDSi      1470 -      1542    8.15     
 1470 -      1541     72
    1 +    5 CDSi      1707 -      1850   11.53     
 1709 -      1849    141
    1 +    6 CDSi      2005 -      2156    2.37     
 2007 -      2156    150
    1 +    7 CDSi      2352 -      2431    7.33     
 2352 -      2429     78
    1 +    8 CDSi      2590 -      2732    5.54     
 2591 -      2731    141
    1 +    9 CDSi      2997 -      3087   14.28     
 2999 -      3085     87
    1 +   10 CDSi      3194 -      3404   22.69     
 3195 -      3404    210
    1 +   11 CDSi      3771 -      4248   40.31     
 3771 -      4247    477
    1 +   12 CDSi      4601 -      4791   11.59     
 4603 -      4791    189
    1 +   13 CDSi      5005 -      5305   37.21     
 5005 -      5304    300
    1 +   14 CDSi      5626 -      5836   22.85     
 5628 -      5834    207
    1 +   15 CDSi      5977 -      7818  139.11     
 5978 -      7816   1839
    1 +   16 CDSi      8124 -      8392   18.83     
 8125 -      8391    267
    1 +   17 CDSi      8588 -      8718   12.84     
 8590 -      8718    129
    1 +   18 CDSi      8947 -      9076    6.48     
 8947 -      9075    129
    1 +   19 CDSi      9177 -      9262   14.21     
 9179 -      9262     84
    1 +   20 CDSi      9444 -      9677   17.54     
 9444 -      9677    234
    1 +   21 CDSi      9819 -      9959   13.12     
 9819 -      9959    141
    1 +   22 CDSi     10061 -     10132    5.47    
 10061 -     10132     72
    1 +   23 CDSi     10399 -     10566   14.32    
 10399 -     10566    168
    1 +   24 CDSi     12282 -     12367   10.06    
 12282 -     12365     84
    1 +   25 CDSi     12476 -     12686   14.76    
 12477 -     12686    210
    1 +   26 CDSi     12858 -     12956    3.52    
 12858 -     12956     99
    1 +   27 CDSi     13063 -     13275   13.29    
 13063 -     13275    213
    1 +   28 CDSi     13390 -     13484    9.79    
 13390 -     13482     93
    1 +   29 CDSi     13584 -     13674   13.39    
 13585 -     13674     90
    1 +   30 CDSl     13783 -     13923   12.35    
 13783 -     13923    141
    1 +      PolA     14083                1.41
 
 Predicted protein(s):
 >FGENESH:   1  30 exon (s)    201  -  13923  2157
 aa, chain +

SDRSGPTAKGKDGKKYSSLNLFDTYKGKSLEIQKPAVAPRHGLQSLGKVAIARRMPPA

LPSLKAENKGNDPNVSLVPKDGTGWASKQEQSDPKSSDASTAQPPESQPLPASQTASN

PKRPPTAPENTPSVPSGVKSWAQASVTHGAHGDGGRASNLLSRFSREEFPTLQAADQD

AAKERESAEQSSGPGPSLRPQNSTTWRDGGGRGPDDLEGPDSKLHHGHDPRGGLQSGP
   ..............
 
 ---
  

=====



Moderated
bionet.genome.gene-structure



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