User talk:Darek Kedra/sandbox 2

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Bioinformatics Dear programs 2 check

  • Spidey
  • Splign
  • est2genome
  • COGs kognitor
  • TIGRFAM curated protein families for microbes
  • GOLD www.genomesonline.org
  • Integr8
  • Genome News Network
  • GenDB Bielefeld
  • genetests.org medical genetic info/GeneReviews


  • Artemis stand alone genome browser


  • PRALINE-PSI - database search method

Gene Prediction

Eukariota

SLAM TWAIN PROJECTOR @Sanger DOUBLESCAN TWINSCAN AAT EVOGENE SGP2

Prokariota

ORPHEUS GLIMMER EASYGENE


Compare

MVISTA

Next

Codon usage database @Kazusa

Pipelines

BABYS PEGASYS BIoMOBY

RNA

tRNA

  • TRNASCAN-SE
  • ARAGORN

SRP RNA

srpscan gu.se

multiple kinds=

Rfam ERPIN

Regulatory sequences DNA=

TRANSFAC DNA-pattern

PATSER search with PWMs MAST

DISCOVERY

YMF MEME ANN-SPEC ALIGNACE MOTIFSAMPLER CONSENSUS

Comparative

FOOTPRINTER PHYLOCON RVISTA

=next

CONREAL

cis- / composite

COMET MSCAN CIS-ANALYST

REGULONDB TRED SCPD

Scan with a motif

PATSER TESS MATCH www.gene-regulation.com OPOSSUM overrepresentation of TF-binding sites

de novo

YMF Teiresias WORDSPY WEEDER MITRA RSAT/Oligo-dyad analysis

de novo PVM

CONSENSUS GIBSS SAMPLER LAWRENCE MEME MOTIFSAMPLER ANN-SPEC ALIGNACE

comparative genomics TF-binding sites

RVISTA CONREAL FOOTER PAP

wustl.edu

Logo generation

ENOLOGOS WEBLOGO

ESTs / Pipelines

EGENE www.icb.usp.br COED ORESTES??

TGICL clustering CLVIEW


map to genome: EXONERATE ESTs clustering tutorial SANBI http://www.sanbi.ac.za/submissionl.PDF

3D

ROSETTA Baker D Robetta

PHOBIUS TRANSMEMBRANE COILS


=Ontology-

CGAP GO Browser AMIGO

GARBAN GODIST BINGO go.tools.microarray.shtml at geneontology.org


FUNCASSOCIATE

COBRA www.xspan.org zooview gofish PANDORA GOBLET Gennav

Go annot www.GENETools.no

goannotator GOTCHA www.compbio.dundee.AC.UK INGOT

GE gene expression tools

  • FUNCASSOCIATE
  • FUNCEEXPRESSION
  • GARBAN
  • GODIST


PROTEIN

PRATT @ EBI 2can


MSA

PRODA.stanford.edu SAGA genetic algorithm MATCH-BOX conserved blox DCA @Bielefield