User talk:Darek Kedra/sandbox 1
Pages to review:
- 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 [1]
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
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
GATA: a graphic alignment tool for comparative sequence analysis
ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
Gene ontology
- Tutorials http://www.geneontology.org/GO.teaching.resources.shtml Very extensiive!
tutorials 2 check
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
- for clusters: PVCLUST R package
http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1540
tree builders
- BioNJ (NJ trees -> same speed better accuracy for large number of taxa)
- http://www.splitstree.org/ SpltsTree4] evolutionary networks from molecular sequence data
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.
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
- 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
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
Portugal
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
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
- 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
- Transcr factors recognition
http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1047
- 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
other courses
Microarray
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
games
folding proteins at foldit: http://fold.it/portal/adobe_main/