The
fast DB documentation
Exons and splicing events definition
BLAST
against EST and mRNA sequence databanks
Alignment
of selected transcript sequence with genomic sequence
Primary definition
of alternative splicing events
Refined definition
of alternative splicing events
Features available from the “Transcripts view” page
Link between
transcripts and PubMed
Prediction of Open
Reading Frames (ORF)
Prediction of
nonsense-mediated mRNA decay (NMD)
Prediction of the
microRNA/transcript interaction sites
Association of
transcript with tissue
Database filling and creation of PDF and SWF files
Multi-alignment of
transcript sequences and in silico
PCR
Multi-alignment
of transcript sequences
Tissue
distribution histogram of all gene transcripts
Tissue
distribution histogram of gene transcripts for a specific event
Analysis of
alternative first exons
Analysis of
alternative terminal exons
Alternative 3’and
5’ splice sites
General information
All scripts have been written in
PERL v5.8.7 (http://www.perl.org/) using the following modules:
- Bioperl (http://www.bio.perl.org/),
- GD (http://www.boutell.com/gd/),
- GD::Graph (http://search.cpan.org/~mverb/GDGraph-1.43/),
- SWF (http://todbot.com/ming/),
- PDF::API2 (http://search.cpan.org/dist/PDF-API2/),
- RTF::Writer (http://search.cpan.org/~sburke/RTF-Writer-1.11/),
- Bio::EnsEMBL (http://www.ensembl.org/),
- HTTP::Lite (http://search.cpan.org/~rhooper/HTTP-Lite-2.1.6/),
- CGI (http://stein.cshl.org/WWW/software/CGI/),
- DBI (http://dbi.perl.org/).
Data processed by our scripts have
been retrieved from the following public databanks:
- EnsEMBL (1) (http://www.ensembl.org/),
- UCSC (2) (http://genomist.ucsc.edu/),
- Genbank (3) (http://www.ncbi.nlm.nih.gov/),
- HUGO (4) (http://www.gene.ucl.ac.uk/nomenclature/),
- CCDS (http://www.ncbi.nlm.nih.gov/CCDS/),
- CGAP (http://cgap.nci.nih.gov/),
- miRBase Targets 2.0