Wikiomics:RNA splicing
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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
