D Hamroun, FO Desmet
and M Lalande

Other analysis
Proceed to an other analysis: splice sites, branch points and cis-elements

Credits & publications
How to cite HSF and mention to softwares used with this program

What's new in this version?
Check the differences between this version and the previous one.

Other bioinformatics tools
Programs made by our team.

Technical requirements & Tips
If you experience problems using HSF, the solution may be in this section.

Questions/suggestions
If you still have problems or inquiries, please contact us.

Human Splicing Finder
Changelog

You can see here all the modifications that have been made on the past and current versions of Human Splicing Finder.

Version 2.4 - November, 12th 2008

Integration of MaxEnt programs from G. Yeo and CB Burge
New matrices added for detecting splicing impact of variants in position +3
Support for indels and duplications in the "Quick mutation" system added
Search database with Consensus CDS
New optional fields added in the submission form: Exon number and Intron number
Use of separate 5' and 3' intronic sequence lengths
SNPs highlighted directly into the sequences in "Analyze mutation(s)" and "Multiple Transcript Analysis"
Minor presentation changes
Bugs fixed

EIE and IIE matrices from Zhang et al. added
"Multiple Transcript Analysis" added. A new analysis type allowing the user to analyze mutants from different transcripts in a single process.
"RefSeq Peptide ID" field added for querying the database
"Quick mutation" system extended to mutants, "Branch point sequence" and "splice site" analysis
SNP search and impact analysis extended to mutants
SNPs highlighted directly into the sequence in "Analyze a sequence", "Branch point sequence" and "splice site analysis"
Line delimiting AGEZ added in branch point analysis
Splicing Sequences Finder (SSF) name changed for Human Splicing Finder (HSF)
Minor presentation changes
Bugs fixed

"Analyze a mutation" and "Analyze mutation(s)" sections are now merged into one section: "Analyze mutation(s)"
Users can choose their thresholds for ESE Finder matrices
New matrix from ESE Finder 3 for SF2/ASF (IgM-BRCA1) added
In batch mutant analysis, extension to intronic substitutions
Deletions and insertions are now allowed in batch mutant analysis and mutant comparison for both exonic and intronic mutations
In batch mutant analysis, duplications and inversions are now allowed (exonic mutations only)
Integration of data from the SNPs databases available on Ensembl
Integration of Exonic Splicing Regulatory sequences from Goren et al.
"Quick mutation" system added, allowing the user to quickly create a mutant from the currently sequence displayed in the "Analyze a sequence" section. Only substitutions, deletions and insertions are permitted for now.
New field for querying the database (Ensembl gene ID) added
Bug fixed