User talk:Darek Kedra/sandbox 1

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Pages to review:


microarrays

databases

overview [1]

Videos bioinformatics

Positive selection

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




microsatellite detection

ESTs clustering

Paper:

Programs:

  • Lucy2 standalone (Win Linux and MacOS)

Sequence assembly with ESTs enhancements=


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

Alternative splicing

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 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

http://bioinformatics.oxfordjournals.org/cgi/content/full/22/12/1540

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.

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

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

ref

Portugal


chip-chip

check (from ringo paper)

MAT [5], TileMap [6],  HGMM [8],

Mass spec progs + sites

metagenomics

Taverna


read

  • 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/

HMM 2 HMM search