Program provides the possibility to search for both donor and acceptor sites, and to define thresholds for them independently. Program allows to search minor variants of splicing donor site (GC-site) as well.

Output example


FSplice 1.0. Prediction of potential splice sites in Homo_sapiens genomic DNA
 Seq name: NM_000449 chr 1 - 148089557 148094091 4535 
 Length of sequence: 4535 
Direct  chain.
 Acceptor(AG) sites. Treshold      4.175 (90%).
       1 P:     187 W:  7.47 Seq: attctAGccctc
       2 P:     296 W:  6.42 Seq: tcttcAGaggct
       3 P:     495 W:  7.30 Seq: tccctAGcagtc
       4 P:     498 W:  5.72 Seq: ctagcAGtcaga
       5 P:     559 W: 14.18 Seq: cccacAGcaagg
       6 P:     847 W:  6.42 Seq: atggtAGcctat
       7 P:    1332 W:  9.70 Seq: acctcAGcaaga
       8 P:    1383 W:  9.25 Seq: ccttcAGctccc
       9 P:    1393 W:  5.38 Seq: ccctcAGgaccc
      10 P:    1673 W:  9.95 Seq: tctgtAGctcag
      11 P:    1721 W:  4.72 Seq: cctatAGgtgga
      12 P:    1916 W:  6.72 Seq: tccctAGggact
      13 P:    1984 W:  9.70 Seq: cactcAGgaagt
      14 P:    2366 W: 12.18 Seq: ctcccAGgtaaa
      15 P:    2467 W:  7.12 Seq: cctgtAGctgag
      16 P:    2638 W:  7.42 Seq: acttcAGccaga
      17 P:    2779 W:  6.42 Seq: gctacAGcagca
      18 P:    2867 W:  6.42 Seq: gtctcAGcaacc
      19 P:    2995 W:  5.03 Seq: ctaccAGtcagt
      20 P:    3033 W:  5.85 Seq: tcctcAGtttcc
      21 P:    3078 W:  9.68 Seq: tctgcAGaagag
      22 P:    3342 W:  9.88 Seq: tttttAGcctcc
      23 P:    3545 W:  8.12 Seq: cccccAGgcttt
      24 P:    4435 W:  6.70 Seq: tcctaAGgaagt
      25 P:    4458 W:  6.65 Seq: tgtacAGacagc
      26 P:    4513 W:  5.65 Seq: ttttcAGcttga
      27 P:    4533 W:  4.58 Seq: gctttAGtg---
 Donor(GT) sites. Treshold      6.099 (90%).
       1 P:      40 W:  8.20 Seq: aagtgGTgagaa
       2 P:     150 W:  7.50 Seq: ccagtGTgagtt
       3 P:     307 W:  7.64 Seq: ccgagGTaccat
       4 P:     317 W:  9.32 Seq: atttcGTaagta
       5 P:     594 W: 15.48 Seq: tcctgGTaagtg
       6 P:     691 W:  9.60 Seq: gagagGTagggt
       7 P:    1416 W: 13.38 Seq: aaaagGTaggtt
       8 P:    1794 W:  7.36 Seq: tatcgGTgggtg
       9 P:    2325 W: 10.44 Seq: agagtGTaagta
      10 P:    2367 W: 13.10 Seq: cccagGTaaaag
      11 P:    2438 W:  8.06 Seq: tctagGTatgat
      12 P:    2841 W:  7.36 Seq: cgctgGTgtgtt
      13 P:    3180 W: 14.08 Seq: cccagGTaagga
      14 P:    3733 W: 10.16 Seq: gagagGTaggca
      15 P:    3796 W:  8.62 Seq: tacctGTgagtg
      16 P:    4177 W: 11.56 Seq: caaaaGTgagtg
      17 P:    4237 W:  6.38 Seq: gagagGTagaca
      18 P:    4341 W:  8.06 Seq: tacagGTctgtg
Reverse chain.
 Acceptor(AG) sites. Treshold      4.175 (90%).
       1 P:     193 W:  6.42 Seq: cccacAGacctg
       2 P:     292 W:  5.40 Seq: ggtgcAGtgtct
       3 P:     316 W:  4.58 Seq: gccaaAGgaaaa
       4 P:     481 W:  8.07 Seq: ttttcAGcctct
       5 P:     517 W: 10.38 Seq: cctccAGctgag
       6 P:     646 W:  4.17 Seq: tttcgAGggcgc
       7 P:     709 W:  7.05 Seq: gctttAGctggt
       8 P:     742 W:  6.70 Seq: ctcacAGgtact
       9 P:    1424 W:  5.67 Seq: ggtttAGatgac
      10 P:    1463 W:  6.97 Seq: tctgcAGaggta
      11 P:    1964 W:  7.45 Seq: ttgtcAGagatc
      12 P:    2035 W:  6.78 Seq: attgcAGaagcc
      13 P:    2068 W:  7.25 Seq: gcctcAGctaca
      14 P:    2287 W:  4.72 Seq: actgtAGcaata
      15 P:    2397 W:  9.20 Seq: ctcccAGgtcct
      16 P:    2421 W:  4.40 Seq: tctctAGtcaag
      17 P:    2748 W:  5.08 Seq: ccgatAGgcatc
      18 P:    2798 W:  5.47 Seq: cttccAGgtggt
      19 P:    3064 W:  6.58 Seq: ttcccAGtgaac
      20 P:    3133 W: 10.05 Seq: tctccAGtggtg
      21 P:    3901 W:  9.50 Seq: ccctcAGcattt
      22 P:    3945 W:  6.03 Seq: ttaccAGgatcc
      23 P:    4298 W:  4.72 Seq: cccccAGtcttg
      24 P:    4406 W: 11.57 Seq: tccccAGaaggc
      25 P:    4440 W:  9.12 Seq: tacccAGaaagg
 Donor(GT) sites. Treshold      6.099 (90%).
       1 P:      31 W:  8.48 Seq: aaaagGTcagag
       2 P:      49 W: 10.02 Seq: accagGTactaa
       3 P:     400 W:  7.08 Seq: ctttgGTatgct
       4 P:     743 W: 10.02 Seq: cacagGTacttc
       5 P:     832 W:  6.80 Seq: gctgaGTgagtc
       6 P:     896 W: 12.40 Seq: agttgGTaagat
       7 P:    1218 W:  7.64 Seq: acacaGTaaggt
       8 P:    1223 W:  8.90 Seq: gtaagGTgtgaa
       9 P:    1466 W:  7.64 Seq: cagagGTaccaa
      10 P:    1477 W: 12.26 Seq: aaaagGTaatag
      11 P:    1491 W: 11.84 Seq: tgaagGTgagga
      12 P:    1830 W:  7.64 Seq: cacagGTcaggg
      13 P:    2196 W:  6.94 Seq: ggaagGTgattt
      14 P:    2686 W:  6.80 Seq: catggGTgaggg
      15 P:    2982 W:  7.22 Seq: ccctgGTaaacc
      16 P:    3159 W:  9.32 Seq: tgaagGTagaga
      17 P:    3209 W: 10.16 Seq: ctgagGTaggag
      18 P:    3773 W:  6.80 Seq: atcaaGTgagag
      19 P:    4253 W:  8.34 Seq: gggtgGTaggtt

Where:

Acceptor(AG) sites. - the type of splicing sites. For the current case "Acceptor(AG)" means the U2-type acceptor site. Possible variants: Donor(GT) sites. means U2-type donor GT-site (Major variant). Donor(GC) sites. means U2-type donor GC- site (Minor variant).

Treshold 4.175 (90%) - means that for the current threshold value (4.175) 90% of true splicing sites are being classified as true.

P: 187 - position of splicing site

W: - weight of site.