User talk:Darek Kedra/sandbox 1

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Pages to review:



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



  • Lucy2 standalone (Win Linux and MacOS)

Sequence assembly with ESTs enhancements=

See also table with less frequently used algorithms:

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


  • 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


tree checks

CONSEL: for assessing the confidence of phylogenetic tree selection Hidetoshi Shimodaira and Masami Hasegawa

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.


  • 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




check (from ringo paper)

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

Mass spec progs + sites




  • 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


  • StarNet find genes with similar expression patterns


  • Transcr factors recognition

  • DIMA] "Domain Interaction MAp and aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains."

Protein 3D

other courses



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

SECIS element / selenocysteine in proteins



folding proteins at foldit:

HMM 2 HMM search