User talk:Darek Kedra/sandbox 2

=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

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