|
FEX Program Description
FEX - (find exons) - Prediction of internal, 5'- and 3'- exons in Human DNA
sequences
Version 2
Method description:
Algorithm first predicts all internal exons in a given sequence by linear discriminant function combining characteristics describing donor and acceptor splice sites, 5'- and 3'-intron regions and also coding regions for each open reading frame flanked by GT and AG base pairs. Potential 5'- and 3'- exons are predicted by corresponding discriminant functions on the left side of the first internal exon and on the right side from last internal exon, respectively.
Accuracy:
The accuracy of precise exon recognition on the set of 210 genes (with 761 internal exons) is 70% with a specificity of 63%. The recognition quality computed at the level of individual nucleotides is 87% for exons sequences (Sp=82%) with the level 97% for intron sequences.
This program does not assemble the exons and is more reliable for a case of missing exons - for example, due to sequencing errors.
FEX output:
First line - name of your sequence
Next lines - positions of predicted exons, their 'weights', ORF number and potential number ORFs for a particular exon.
For example:
Seq name: Adh_and_cact.1 (2919020 bases) 848501 853000
Length of sequence: 4500 Exon thr- 0 Overlap thr- 0.0
# of potential exons: 9
2758 - 2936 + w= 27.96 ORF= 0 First exon 2758 - 2934
3291 - 3354 - w= 13.63 ORF= 2 First exon 3292 - 3354
2577 - 2690 + w= 11.78 ORF= 2 Internal exon 2579 - 2689
3 - 269 + w= 10.06 ORF= 0 Single exon 3 - 269
3024 - 3107 - w= 9.15 ORF= 2 Internal exon 3025 - 3105
385 - 543 + w= 2.22 ORF= 0 Last exon 385 - 543
3169 - 3173 + w= 2.18 ORF= 0 First exon 3169 - 3171
2213 - 2380 + w= 1.65 ORF= 0 Last exon 2213 - 2380
1037 - 1076 + w= 0.25 ORF= 0 First exon 1037 - 1075
>Exon- 1 Amino acid sequence - 59 aa, chain +
MANCPHTIGVEFGTRIIEVDDKKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITR
>Exon- 2 Amino acid sequence - 21 aa, chain -
MACAELRTRRRSDRADPPGCS
>Exon- 3 Amino acid sequence - 37 aa, chain +
PNMTAAPYNYNYIFKYIIIGDMGVGKSCLLHQFTEKK
>Exon- 4 Amino acid sequence - 88 aa, chain +
MLVQTPGISKSWMSSICLRESTFFMSCDRFRRSVSHCEGDTHELTAWQRVYLATHIWHRL
AGAQVVDLHIVNFVYEHLEGRFLLKIKT
>Exon- 5 Amino acid sequence - 27 aa, chain -
NLPSALQIRFVANEKDHSAGIGEIASV
>Exon- 6 Amino acid sequence - 52 aa, chain +
CDRRKPSKTRERKSSEKRLLICIDLPIENNRNNCLSVQPRNPAKPVCVLARK
>Exon- 7 Amino acid sequence - 1 aa, chain +
M
>Exon- 8 Amino acid sequence - 55 aa, chain +
LAGKQTRSAVQTQAGLKKKYRGQFEKGEQNVVSTQNKLMQRLGLLISSDYGWTFK
>Exon- 9 Amino acid sequence - 13 aa, chain +
MVGQKRPPLYLKI
Reference:
Solovyev V.V.,Salamov A.A., Lawrence C.B.
Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.
(Nucl.Acids Res.,1994,22,24,5156-5163).
Solovyev V.V., Salamov A.A. , Lawrence C.B.
The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.
in: The Second International conference on Intelligent systems for Molecular Biology (eds. Altman R., Brutlag D., Karp R., Latrop R. and Searls D.), AAAI Press, Menlo Park, CA (1994, 354-362)
|