Darek Kedra: +Category

Darek Kedra — Tue, 29 Jul 2008 17:58:18 GMT

+Category

←Older revision		Revision as of 17:58, 29 July 2008
Line 43:		Line 43:
	* [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
		+
		+
		+	[[Category:Protocol]]
		+	[[Category:In silico]]
		+	[[Category:Sequence analysis]]

Darek Kedra: /* Alternative splice forms databases: */ link fix

Darek Kedra — Tue, 08 Jul 2008 14:18:49 GMT

Alternative splice forms databases:: link fix

←Older revision		Revision as of 14:18, 8 July 2008
Line 23:		Line 23:
	==Alternative splice forms databases:==		==Alternative splice forms databases:==
	Recommended:		Recommended:
-	* [www.ensembl.org ENSEMBL] not the most extensive but first choice for typical, already detected transcripts in a number of species	+	* [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)

Darek Kedra: splicing (first draft)

Darek Kedra — Tue, 24 Jun 2008 10:18:39 GMT

splicing (first draft)

New page

=Splicing=

Review paper: [http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0040021 Holste@PLOS 2008]



=ESTs or mRNA to genome mapping software=
* [http://www.biozentrum.unibas.ch/~nimwegen/cgi-bin/spa.cgi SPA] climed to be more acurate than GMAP, uses blat server for a fast sequence mapping/retrieval and creates its own cDNA/genome alignment.
* [http://www.gene.com/share/gmap GMAP] standalone. Fast, good at mapping transcripts + alignment. Detects microexons. Output also in GFF format

* [http://www.well.ox.ac.uk/~rmott/ESTGENOME/est_genome.shtml EST_GENOME] standalone program. Good at mapping / aligning, not good for alternative splice forms from ESTs?

*[http://blast.wustl.edu/exalin EXALIN] mRNA not multiple ESTs?
* [http://deepc2.psi.iastate.edu/cgi-bin/gs.cgi GENESEQER] web server several organisms and splice models. allows generic splice, user provided genomic sequence & ESTs collection
* [http://globin.cse.psu.edu/html/docs/sim4.html SIM4] accurate in tests (see SPA paper), used by ASP?
* [http://origin.bic.nus.edu.sg/mgalign/ MGALIGN] web server does not accept cDNA sequences longer than genomic sequence (no multiple ESTs?)
* [http://www.ncbi.nlm.nih.gov/spidey SPIDEY] web server @NCBI + stand alone binaries for several platforms
* [http://hgwdev-hiram.cse.ucsc.edu/IntronWS120/index.html 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

* [http://statgen.ncsu.edu/asg/ ASG] Alternative splicing Galery. Human only. Based on splicing graphs (1.2 milions transcripts)
* [http://www.ebi.ac.uk/astd/main.html Alternative Splicing and Transcript Diversity @EBI] human, mouse and rat only
* [http://t.caspur.it/ASPIC/ ASPIC] web server

to check:

* [http://helios.informatik.uni-freiburg.de/TassDB/ TassDB] alternative splice events at GYNGYN donors and NAGNAG acceptors in 8 speces
* [http://hollywood.mit.edu/Logo/index.html hollywood@MIT] H.sapiens + mouse only
* [http://bioinformatics.ucla.edu/ASAP2/ ASAP II] splicing DB of several species from 2006.
* [http://prosplicer.mbc.nctu.edu.tw/ ProSplicer] An Alternative Splicing Database based on Protein, mRNA, and EST Sequences (human only??)
* [http://splicenest.molgen.mpg.de/ SpliceNest] visualization of mappings of EST Contigs to genomic sequence (human, mouse, arabidopsis, drosopghila only)

==APIs==
* [http://bioinfo.mbi.ucla.edu/pygr Pygr] python graph library used @UCLA

== est translations ==
* [http://www.ch.embnet.org/software/ESTScan2.html ESTScan2]
* [http://www.ncbi.nlm.nih.gov/pubmed/11673235 diana-est] request by email

Wikiomics:RNA splicing - Revision history

Darek Kedra: +Category

Darek Kedra: /* Alternative splice forms databases: */ link fix

Darek Kedra: splicing (first draft)