HomeAll softwareProductsNew ProductsServicesManagement teamCorporate ProfileContact

Test online

Gene finding
Gene finding with similarity
Gene finding in Bacteria
Gene finding in Viruses
Next Generation
Gene search
Gene explorer
Promoter
Protein location
RNA structure
Protein structure
3d-explorer
SeqMan
Multiple alignment
Analysis of expression data
Plant promoter database
Search and map repeats
Extracting known SNPs

 

 

FSPLICE Program Description

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.

© 2021 www.softberry.com