Wikiomics:RNA splicing

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==Alternative splice forms databases:==  
==Alternative splice forms databases:==  
Recommended:
Recommended:
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* [www.ensembl.org ENSEMBL] not the most extensive but first choice for typical, already detected transcripts in a number of species
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* [http://www.ensembl.org ENSEMBL] not the most extensive but first choice for typical, already detected transcripts in a number of species
* [http://statgen.ncsu.edu/asg/ ASG] Alternative splicing Galery. Human only. Based on splicing graphs (1.2 milions transcripts)  
* [http://statgen.ncsu.edu/asg/ ASG] Alternative splicing Galery. Human only. Based on splicing graphs (1.2 milions transcripts)  
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* [http://www.ch.embnet.org/software/ESTScan2.html ESTScan2]
* [http://www.ch.embnet.org/software/ESTScan2.html ESTScan2]
* [http://www.ncbi.nlm.nih.gov/pubmed/11673235 diana-est] request by email
* [http://www.ncbi.nlm.nih.gov/pubmed/11673235 diana-est] request by email
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[[Category:Protocol]]
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[[Category:In silico]]
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[[Category:Sequence analysis]]

Current revision

Contents

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

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

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