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FGENESH - Program for predicting multiple genes in genomic DNA sequences

FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff et al. (2002) Science 296:79).

 

   

(above) Performance of different gene finding programs on rice genes. Reprinted from Yu et al. (2002) Science 296:79-92. FGENESH is by far the most accurate of five programs tested.

(Below) Performance of three popular gene prediction programs on 42 semiartificial genomic sequences containing 178 known human gene sequences (900 exons). Sensitivity is percentage of exons that are predicted correctly. Selectivity is percentage of predicted exons that are correct. Reproduced with changes from Yada et al., 2002 Cold Spring Harbor Genome Sequencing and Biology Meeting, May 7-11, 2002. FGENESH is by far the most accurate of three programs.

Program
Sensitivity
Specificity
Missed Exons, %
Wrong Exons, %
FGENESH
77.1
65.7
9.6
23.2
GenScan
66.5
44.9
12.0
40.9
HMMGene
69.6
36.6
15.5
55.5

 

Web version of FGENESH can be used with parameters for the following genomes: human, mouse, Drosophila, nematode, dicot plants, monocot plants, yeast (S.pombe) and Neurospora.

Check appropriate genome/organism and and FGENESH program. Paste your sequence to the window or load your file with sequence in FASTA format and click Perform Search button.

References: Salamov A., Solovyev V. (2000)
Ab initio gene finding in Drosophila genomic DNA.
Genome Res., 10,516-522

Fgenesh output:
G - predicted gene number, starting from start of sequence;
Str - DNA strand (+ for direct or - for complementary);
Feature - type of coding sequence: CDSf - First (Starting with Start codon), CDSi - internal (internal exon), CDSl - last coding segment, ending with stop codon);
TSS - Position of transcription start (TATA-box position and score);
Start and End - Position of the Feature;
Weight - Log likelihood*10 score for the feature;
ORF - start/end positions where the first complete codon starts and the last codon ends.

FGENESH-2.1 Prediction of potential genes in genomic DNA
Time:   Thu Jan 28 19:25:51 1999.
Seq name: HUMHBB      73308 bp    DNA             PRI       20-JAN-1994        
length of sequence  73308bp  G+C content: 39 Isochore: 1
number of predicted genes 7 in +chain 7 in -chain 0
number of predicted exons 18 in +chain 18 in -chain 0

  Gn S   Type   Start       End   Score        ORF           Len
  -- -   ----   -----       ---   -----        ---           ---
   1 +   TSS    19447             -7.15  
   1 +   CDSf   19541 -   19632   16.12   19541 -   19630     90
   1 +   CDSi   19755 -   19977   14.12   19756 -   19977    222
   1 +   CDSl   20833 -   20961    2.99   20833 -   20961    129
   1 +   PolA   21055              1.05  

   2 +   TSS    34437             -7.15  
   2 +   CDSf   34531 -   34622   15.25   34531 -   34620     90
   2 +   CDSi   34745 -   34967   20.74   34746 -   34967    222
   2 +   CDSl   35854 -   35982    5.59   35854 -   35982    129
   2 +   PolA   36043              1.05  

   3 +   TSS    39373             -7.15  
   3 +   CDSf   39467 -   39558   15.25   39467 -   39556     90
   3 +   CDSi   39681 -   39903   20.74   39682 -   39903    222
   3 +   CDSl   40770 -   40898    5.74   40770 -   40898    129
   3 +   PolA   40959              1.05  

   4 +   TSS    44415             -8.75  
   4 +   CDSf   45995 -   46151   16.01   45995 -   46150    156
   4 +   CDSl   46997 -   47100    2.71   46999 -   47100    102
   4 +   PolA   47243              1.05  

   5 +   TSS    54703             -4.45  
   5 +   CDSf   54790 -   54881   13.41   54790 -   54879     90
   5 +   CDSi   55010 -   55232   14.20   55011 -   55232    222
   5 +   CDSl   56131 -   56259    3.87   56131 -   56259    129
   5 +   PolA   56365              1.05  

   6 +   TSS    62100             -6.65  
   6 +   CDSf   62187 -   62278   13.59   62187 -   62276     90
   6 +   CDSi   62409 -   62631   19.50   62410 -   62631    222
   6 +   CDSl   63482 -   63610   10.23   63482 -   63610    129
   6 +   PolA   63718              1.05  

   7 +   TSS    68088             -9.45  
   7 +   CDSo   68183 -   68428   14.87   68183 -   68428    246
   7 +   PolA   68509              1.05  

Predicted protein(s):
>ID  1   3 exon (s)  19541  -  20961    147 aa, chain +
MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK
VKAHGKKVLTSFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG
KEFTPEVQAAWQKLVSAVAIALAHKYH
>ID  2   3 exon (s)  34531  -  35982    147 aa, chain +
MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
KEFTPEVQASWQKMVTGVASALSSRYH
>ID  3   3 exon (s)  39467  -  40898    147 aa, chain +
MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
KEFTPEVQASWQKMVTAVASALSSRYH
>ID  4   2 exon (s)  45995  -  47100     86 aa, chain +
MGNPKVKAHGKKVLISFGKAVMLTDDLKGTFATLSDLHCNKLHVDPENFLVSTLRQRDID
CFGNPLQRGFYPTDTGFLAVTNKCCG
>ID  5   3 exon (s)  54790  -  56259    147 aa, chain +
MVHLTPEEKTAVNALWGKVNVDAVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPK
VKAHGKKVLGAFSDGLAHLDNLKGTFSQLSELHCDKLHVDPENFRLLGNVLVCVLARNFG
KEFTPQMQAAYQKVVAGVANALAHKYH
>ID  6   3 exon (s)  62187  -  63610    147 aa, chain +
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK
VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG
KEFTPPVQAAYQKVVAGVANALAHKYH
>ID  7   1 exon (s)  68183  -  68428     81 aa, chain +
MEQSWAENDFDELREEGFRRSNYSKLKEEVRTNGKEVKNFEKKLDEWITRITNAQKSLKD
LMELKTKAGELRDKYTSLSNR
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