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Fgenes |
Pattern based human gene structure prediction (multiple genes, both chains).
Method description:
Algorithm based on pattern recognition of different types of exons,
promoters and polyA signals. Optimal combination of these features is then found by dynamic
programming and a set of gene models is constructed along a given sequence.
Fgenes output:
G - predicted gene number, starting from start of sequence;
Str - DNA strand (+ for direct and - for complementary strands);
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);
TSS - position of transcription start;
TATA – position of TATA-box;
wTATA – Discriminant function score for TATA box;
Start and End - Positions of the Feature;
Weight - Discriminant function score for the feature;
ORF - start/end positions of ORF where the first complete codon starts and the last codon ends.
FGENES 1.5 Prediction of multiple genes in genomic DNA
Time: 171940.7 Date: 20001003
Seq name: > HUMHBB 73308 bp DNA PRI 20-JAN-1
Length of sequence: 73308 GC content: 0.39 Zone: 1
Number of predicted genes: 9 In +chain: 7 In -chain: 2
Number of predicted exons: 23 In +chain: 19 In -chain: 4
Positions of predicted genes and exons:
G Str Feature Start End Weight ORF-start ORF-end
1 - 1 CDSi 5978 - 6039 1.69 5978 - 6037
1 - 2 CDSf 6314 - 6365 1.40 6315 - 6365
2 - 1 CDSl 13709 - 13807 1.84 13712 - 13807
2 - 2 CDSf 14781 - 14855 1.62 14781 - 14855
3 + TSS 19488 5.83 TATA 19457 wTATA 19.85 LDF 0.81
3 + 1 CDSf 19541 - 19632 11.08 19541 - 19630
3 + 2 CDSi 19755 - 19977 6.20 19756 - 19977
3 + 3 CDSl 20833 - 20961 5.95 20833 - 20958
3 + PolA 21055 2.08
4 + TSS 34478 4.98 TATA 34447 wTATA 19.21 LDF 0.91
4 + 1 CDSf 34531 - 34622 8.82 34531 - 34620
4 + 2 CDSi 34745 - 34967 5.96 34746 - 34967
4 + 3 CDSl 35854 - 35982 6.30 35854 - 35979
4 + PolA 36043 2.68
5 + TSS 39412 5.00 TATA 39383 wTATA 19.21 LDF 0.93
5 + 1 CDSf 39467 - 39558 8.82 39467 - 39556
5 + 2 CDSi 39681 - 39903 5.96 39682 - 39903
5 + 3 CDSl 40770 - 40898 6.17 40770 - 40895
5 + PolA 40959 2.78
6 + 1 CDSf 45995 - 46151 3.09 45995 - 46150
6 + 2 CDSl 46997 - 47100 2.32 46999 - 47097
6 + PolA 47243 2.75
7 + 1 CDSf 54790 - 54881 8.97 54790 - 54879
7 + 2 CDSi 55010 - 55232 5.60 55011 - 55232
7 + 3 CDSl 56131 - 56259 5.05 56131 - 56256
7 + PolA 56365 1.07
8 + 1 CDSf 62187 - 62278 9.72 62187 - 62276
8 + 2 CDSi 62409 - 62631 6.64 62410 - 62631
8 + 3 CDSl 63482 - 63610 6.56 63482 - 63607
8 + PolA 63718 4.72
9 + 1 CDSf 68183 - 68290 2.50 68183 - 68290
9 + 2 CDSl 70703 - 70819 1.10 70703 - 70816
9 + PolA 70905 4.71
Predicted proteins:
>FGENES 1.5 > HUMHBB 7 1 Multiexon gene 5978 - 6365 38 a Ch-
MVCNCGLDHNFQSPRSKTCAFNKLIYTTSTLGSSSINE
>FGENES 1.5 > HUMHBB 7 2 Multiexon gene 13709 - 14855 57 a Ch-
MCSHHLASNCCFRSVPLPHLSRSLQEFVLKVNFHNRKLIEAKASVKERNISSKPLCC
>FGENES 1.5 > HUMHBB 7 3 Multiexon gene 19541 - 20961 147 a Ch+
MVHFTAEEKAAVTSLWSKMNVEEAGGEALGRLLVVYPWTQRFFDSFGNLSSPSAILGNPK
VKAHGKKVLTSFGDAIKNMDNLKPAFAKLSELHCDKLHVDPENFKLLGNVMVIILATHFG
KEFTPEVQAAWQKLVSAVAIALAHKYH
>FGENES 1.5 > HUMHBB 7 4 Multiexon gene 34531 - 35982 147 a Ch+
MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
KEFTPEVQASWQKMVTGVASALSSRYH
>FGENES 1.5 > HUMHBB 7 5 Multiexon gene 39467 - 40898 147 a Ch+
MGHFTEEDKATITSLWGKVNVEDAGGETLGRLLVVYPWTQRFFDSFGNLSSASAIMGNPK
VKAHGKKVLTSLGDAIKHLDDLKGTFAQLSELHCDKLHVDPENFKLLGNVLVTVLAIHFG
KEFTPEVQASWQKMVTAVASALSSRYH
>FGENES 1.5 > HUMHBB 7 6 Multiexon gene 45995 - 47100 86 a Ch+
MGNPKVKAHGKKVLISFGKAVMLTDDLKGTFATLSDLHCNKLHVDPENFLVSTLRQRDID
CFGNPLQRGFYPTDTGFLAVTNKCCG
>FGENES 1.5 > HUMHBB 7 7 Multiexon gene 54790 - 56259 147 a Ch+
MVHLTPEEKTAVNALWGKVNVDAVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPK
VKAHGKKVLGAFSDGLAHLDNLKGTFSQLSELHCDKLHVDPENFRLLGNVLVCVLARNFG
KEFTPQMQAAYQKVVAGVANALAHKYH
>FGENES 1.5 > HUMHBB 7 8 Multiexon gene 62187 - 63610 147 a Ch+
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPK
VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFG
KEFTPPVQAAYQKVVAGVANALAHKYH
>FGENES 1.5 > HUMHBB 7 9 Multiexon gene 68183 - 70819 74 a Ch+
MEQSWAENDFDELREEGFRRSNYSKLKEEVRTNGKEASIILIPKPDRDTTKKENVTPISL
MNIDAKILNKILAN