SpliceScanII scoring putative internal exons
This program is further improved tool SpliceScan, where we score splice sites based on exon definition model, which includes simultaneous scoring of acceptor and donor signals, exon length distribution and contribution of Exonic/Intronic Enhancer/Silencer elements associated with the delicate balance of factors committing exons to splicing. All the scoring happens through Bayesian rule in terms of LODs (Logarithm Of Odds), where the LOD is the logarithm base 2 of the signal concentration ratio in vicinity of a true versus decoy splice site. Please refer to our publication on SpliceScan II for further details:
Alexander Churbanov, Igor Vorechovsky and Chindo Hicks A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements, BMC Bioinformatics 2010, 11:22Presentation made at BIG is available here.
Please input pre-mRNA nucleotide sequences, which you would like to score in FASTA format. Your input should look similar to this where the homology-based gene structural annotation for this fragment could be found here. FASTA id, number of sequences and comments may vary. Please remember that pre-mRNA is a single-stranded molecule, therefore if gene is located on anti-sense strand the pre-mRNA orientation should be reverse compliment of the containing DNA locus. Also, in your submission please allow 400 nt or more at the intronic flanks for an exon of interest. Shorter flanks might not work well for the prediction purposes.
The resulting prediction displays in the format shown below, where
TEST4 stands for FASTA ID of a sequence we examine, putative
internal exon predicted has start and end indexes within the sequence,
overall LOD score normalized according to the true exonic human LOD score
distribution histogram in the range [0,1] where, for example, 0 is the weakest
possible score assigned to a putative exon still to be considered as true.
The LOD score features within
* entries are donor, acceptor and exonic length
scores. Donors and acceptors have normalized scores coming from the Bayesian splice site
sensor with their translation to the corresponding LOD score. Normally, stronger
splice sites can comfort shorter exons, so that we score the exonic length
according to the histograms recorded for various splice sites strength combination.
All the options in + marked entries are either the
LOD score for competing splice sites trying to destabilize the exonic boundaries
or the LOD scores for the Enhancers/Silencers.
Input your query in FASTA format here:
|Note: SpliceScan II is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.|