Wikiomics:RNA splicing

=Splicing=

Review paper: Holste@PLOS 2008

=ESTs or mRNA to genome mapping software=
 * SPA climed to be more acurate than GMAP, uses blat server for a fast sequence mapping/retrieval and creates its own cDNA/genome alignment.
 * GMAP standalone. Fast, good at mapping transcripts + alignment. Detects microexons. Output also in GFF format


 * EST_GENOME standalone program. Good at mapping / aligning, not good for alternative splice forms from ESTs?


 * EXALIN mRNA not multiple ESTs?
 * GENESEQER web server several organisms and splice models. allows generic splice, user provided genomic sequence & ESTs collection
 * SIM4 accurate in tests (see SPA paper), used by ASP?
 * MGALIGN web server does not accept cDNA sequences longer than genomic sequence (no multiple ESTs?)
 * SPIDEY web server @NCBI + stand alone binaries for several platforms
 * Intronerator by Jim Kent, 1999

Alternative splice forms databases:
Recommended:
 * ENSEMBL not the most extensive but first choice for typical, already detected transcripts in a number of species


 * ASG Alternative splicing Galery. Human only. Based on splicing graphs (1.2 milions transcripts)
 * Alternative Splicing and Transcript Diversity @EBI human, mouse and rat only
 * ASPIC web server

to check:


 * TassDB alternative splice events at GYNGYN donors and NAGNAG acceptors in 8 speces
 * hollywood@MIT H.sapiens + mouse only
 * ASAP II splicing DB of several species from 2006.
 * ProSplicer An Alternative Splicing Database based on Protein, mRNA, and EST Sequences (human only??)
 * SpliceNest visualization of mappings of EST Contigs to genomic sequence (human, mouse, arabidopsis, drosopghila only)

APIs

 * Pygr python graph library used @UCLA

est translations

 * ESTScan2
 * diana-est request by email