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:

• [www.ensembl.org 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