Trop Team
Search Harland trop site
Obtain Embryos
Genomic Resources
Trop Labs

Genomic Resources on the Web

Genome Databases and Browsers

Genome Evolutionary Comparative Tools

Alignment Tools

Transcription Binding Factor Site Tools

Phylogenetic Footprinting

Pattern Finding

Clustering of TFBS or Motifs

Clustering of Motifs upstream of Coexpressed Genes from Microarray Data

PCR Primer Design

Molecular Biology

ECR Browser http://ecrbrowser.dcode.org/
rVISTA http://rvista.dcode.org/
eShadow http://eshadow.dcode.org/

Genome Databases and Browsers
BDGP http://www.fruitfly.org/
Ensembl http://www.ensembl.org/
ExoFish http://www.genoscope.cns.fr/externe/tetraodon/
FlyBase http://flybase.bio.indiana.edu/
GRAMENE http://www.gramene.org/
HGSC_Baylor http://www.hgsc.bcm.tmc.edu/
JGI http://genome.jgi-psf.org/
MGD http://www.informatics.jax.org/
NCBI http://www.ncbi.nlm.nih.gov/
NISC http://www.nisc.nih.gov/
Rat Genome http://www.rgd.mcw.edu/
Sanger http://www.sanger.ac.uk/
SGD http://genome-www.stanford.edu/Saccharomyces/
TAIR http://www.arabidopsis.org/
TIGR http://www.tigr.org/
UCSC http://www.genome.ucsc.edu/
Wormbase http://www.wormbase.org/

Genome Comparative Analysis Tools Genomic Sequences from:
ECR Browser http://ecrbrowser.dcode.org/ human/mouse/fugu
GALA http://globin.cse.psu.edu/ human/mouse
Penn State http://bio.cse.psu.edu/genome/hummus/ human/mouse
UCSC http://www.genome.ucsc.edu/ human/mouse/rat
VISTA http://pipeline.lbl.gov/ human/mouse/rat

Alignment Tools
Alfresco http://www.sanger.ac.uk/Software/Alfresco/
AVID http://baboon.math.berkeley.edu/mavid/
BALSA http://bayesweb.wadsworth.org/balsa/balsa.html
BLAST http://www.ncbi.nlm.nih.gov/BLAST/
Blast2Sequences http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html
BLAT http://genome.ucsc.edu/cgi-bin/hgBlat
BLOCKS http://blocks.fhcrc.org/
ClustalW http://www.ebi.ac.uk/clustalw/
DIALIGN2 http://www.gsf.de/biodv/dialign.html
EMBOSS http://www.ebi.ac.uk/emboss/align/
GLASS http://glass.lcs.mit.edu/
LAGAN http://lagan.stanford.edu/
LALIGN http://www.ch.embnet.org/software/LALIGN_form.html
MUMmer http://www.tigr.org/software/mummer/
Pattern Hunter http://www.bioinformaticssolutions.com/products/ph.php
Pfam http://www.sanger.ac.uk/Software/Pfam/
PipMaker http://bio.cse.psu.edu/pipmaker/
Poa http://www.bioinformatics.ucla.edu/poa/POA_Online/Align.html
SAM http://www.cse.ucsc.edu/research/compbio/sam.html
SSAHA http://www.sanger.ac.uk/Software/analysis/SSAHA/
SSEARCH http://www.biology.wustl.edu/gcg/ssearch.html
SynPlot http://www.sanger.ac.uk/Users/jgrg/SynPlot
Tcoffee http://www.ch.embnet.org/software/TCoffee.html
VISTA http://www-gsd.lbl.gov/VISTA/index.html
WUBlast2 http://www.ebi.ac.uk/blast2/

Transcription Factor Binding Site Analysis
CIS-ANALYST http://rana.lbl.gov/cis-analyst/
CONSITE http://forkhead.cgr.ki.se/cgi-bin/consite
RVISTA http://rvista.dcode.org/
TESS http://www.cbil.upenn.edu/tess/
TRANSFAC http://www.biobase.de/

Phylogenetic Footprinting
FootPrinter http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput2.pl
TRES http://bioportal.bic.nus.edu.sg/tres/
EShadow http://eshadow.dcode.org/

Pattern Finding
AlignACE http://atlas.med.harvard.edu/
ANN-Spec http://www.cbs.dtu.dk/services/DNAarray/ann-spec.html
CONSENSUS http://www.bork.embl-heidelberg.de/Alignment/consensus.html
MEME http://meme.sdsc.edu/meme/website/intro.html

Clustering of TFBS or Motifs
CIS-ANALYST http://rana.lbl.gov/cis-analyst/
Cister http://zlab.bu.edu/~mfrith/cister.shtml
GALA http://gala.cse.psu.edu/
RVISTA http://rvista.dcode.org/
TFCLUSTER http://stateslab.bioinformatics.med.umich.edu/service/tfcluster/
TraFaC http://trafac.chmcc.org

Clustering of Motifs upstream of Coexpressed Genes from Microarray Data
BioProspector http://bioprospector.stanford.edu/
CREME http://creme.dcode.org/

Primer Design
CODEHOP (degenerate primers) http://blocks.fhcrc.org/codehop.html
Primer3 http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
PrimerX (mutagenic primers) http://bioinformatics.org/primerx/

Molecular Biology
ORF http://www.ncbi.nlm.nih.gov/gorf/gorf.html
Reverse Complement http://bioinformatics.org/sms/rev_comp.html
Restriction Enzymes (NEB) http://tools.neb.com/NEBcutter2/index.php
EST Assembler http://bio.ifom-firc.it/ASSEMBLY/assemble.html


Thanks to Gabby for putting together this list.