Version 2
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.
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.
First line - name of your sequence
Next lines - positions of predicted exons, their 'weights', ORF number and potential number ORFs for a particular exon.
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
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)