User talk:Darek Kedra/sandbox 1

Pages to review:

 * http://www.bioalgorithms.info/slides.php


 * http://www.biomedcentral.com/1471-2105/7/499 (sequence alignment refinement paper)


 * http://nar.oxfordjournals.org/cgi/content/full/33/22/7120 Automatic assessment of alignment quality


 * ftp://ftp-igbmc.u-strasbg.fr/pub/RASCAL RASCAL 1.1


 * http://www.dbi.tju.edu/dbi/index.php?menu=42 PAINT promoter database


 * http://www.pdg.cnb.uam.es/fabascal/ tutorials ++

microarrays

 * http://depts.washington.edu/l2l/ Database of up/down regulated genes

databases

 * http://base.thep.lu.se/ BASE
 * http://www.longhornarraydatabase.org/ LAD
 * http://genome.tugraz.at/mars/mars_description.shtml MARS (2006) (doc HTML)
 * http://www.sbeams.org/Microarray/ SBEAMS

overview

=Videos bioinformatics=
 * http://calit2.net/events/algorithmicbio/archive.php San Diego ALGORITHMIC BIOLOGY 2006

=Positive selection= How to detect a pssitive selection of certain AA in a set of homologues sequences?:


 * Selection (WEB) (requires >=5 ORFs + query ORF. Can handle PDB files
 * SWAKK (WEB)
 * SWAPSC (standalone Win and Linux) PHYLIP formated input

=microsatellite detection=
 * SciRoKo article

=ESTs clustering= Paper:


 * EMBnet course (PDF)

Programs:
 * Lucy2 standalone (Win Linux and MacOS)

Sequence assembly with ESTs enhancements

 * MIRA2 also detects SNPs

See also table with less frequently used algorithms: http://biolinfo.org/EST/assembly.htm

Alternative splicing

 * ASTRA (Alternative Splicing and TRanscription Archives)
 * ECgene Genome Annotation for Alternative Splicing. Large number of putative splice forms.

=Sequence comparisons=

Genomic DNA

 * PipMaker
 * MultiPipMaker http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=168985

GATA: a graphic alignment tool for comparative sequence analysis
 * GATA paper

ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
 * ESPERR

=Gene ontology=
 * Tutorials http://www.geneontology.org/GO.teaching.resources.shtml Very extensiive!

tutorials 2 check

 * http://biophilessurf.info/tutorials.html

Blast tabulated output
Columns:
 * Identity of query sequence
 * Identity of subject sequence (matching sequence in database)
 * Percent identity
 * Alignment length
 * Number of mismatches
 * Number of gaps
 * Start of query sequence
 * End of query sequence
 * Start of subject sequence
 * End of subject sequence
 * E-value
 * Bit-score

=Phylogeny=

tree checks
CONSEL: for assessing the confidence of phylogenetic tree selection Hidetoshi Shimodaira and Masami Hasegawa http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1246
 * CONSEL

http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1540
 * for clusters: PVCLUST R package

tree builders

 * BioNJ (NJ trees -> same speed better accuracy for large number of taxa)

phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.
 * http://www.splitstree.org/ SpltsTree4] evolutionary networks from molecular sequence data

alignments

 * PANDIT database of multiple sequence alignments and phylogenetic trees covering many common protein domains.

protein phylogeny align

 * Quality estimation of multiple sequence alignments by Bayesian hypothesis testing web server HTML


 * BAli-Phy HTML


 * DCA


 * GramAlign fast aligner. No ALN output

2 read
DIVERGE: phylogeny-based analysis for functional–structural divergence of a protein family Gu * and Kent Vander Velden

=genome variants DB =


 * TCAG curated catalogue of structural variation in the human genome

=stuff to incorporate =


 * http://en.wikipedia.org/wiki/User:Darked/ABRF_2005

=Protein vs mRNA level differences=

Protein vs mRNA level deifferences

Stability of mRNA

 * Decapping of mRNA
 * Deandenylation

Regulation of translation

 * number of ribbosomes per mRNA transcript
 * binding of specific RBP (RNA binding proteins) to mRNA

=EST 2 genome alignment= ref
 * PALMA

Portugal

 * courses to check

chip-chip
check (from ringo paper) MAT [5], TileMap [6], HGMM [8],

Mass spec progs + sites

 * http://proteome.gs.washington.edu/
 * MyriMatch http://pubs.acs.org/cgi-bin/abstract.cgi/jprobs/2007/6/i02/abs/pr0604054.html
 * MyriMatch http://www.mc.vanderbilt.edu/msrc/bioinformatics/
 * http://mass-spec.lsu.edu/blog/ Mass Spec blog

metagenomics

 * Strainer http://www.biomedcentral.com/1471-2105/8/398

Taverna

 * collection of workflows http://myexperiment.org/

read

 * http://wiki.molecularstation.com/index.php?title=Translation_Termination
 * Graphs /networks http://jcs.biologists.org/cgi/content/full/118/21/4947
 * Bioclipse cheminformatics based on eclipse http://wiki.bioclipse.net/index.php?title=Main_Page
 * http://www.genome.org/cgi/content/abstract/13/6a/1222


 * ARB (used by Venter for metagenomics projects)

CHECK SERVERS 3D/align evol trace

 * http://www-cryst.bioc.cam.ac.uk/servers.html FUGUE...


 * Parepro 2007 SVM, server
 * MAPP evolutionary trace program java
 * SNPs3D assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis.
 * PMut annotation and prediction of pathological mutations

Expression/networks:
 * StarNet find genes with similar expression patterns

check
http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1047
 * Transcr factors recognition


 * http://mips.gsf.de/genre/proj/dima2/ DIMA] "Domain Interaction MAp and aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains."

Protein 3D

 * http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=16526955

other courses

 * http://www.swbic.org/education/courses.php

Microarray

 * comparisons (Järvinen)

=Metabolomics= Wishart, David S. “Current Progress in computational metabolomics.” Brief Bioinform (July 11, 2007): bbm030. HTML

SECIS element / selenocysteine in proteins
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1914089

motif/gramar

 * http://adios.tau.ac.il/algorithm.html

=games= folding proteins at foldit: http://fold.it/portal/adobe_main/

HMM 2 HMM search

 * HHSenser