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INFORMATION FOR

Science Tools

Alignment tools

Alfresco https://www.sanger.ac.uk/resources/software/alfresco/
BALSA https://www.wadsworth.org/research/scientific-resources
BLAST https://www.ncbi.nlm.nih.gov/BLAST/
Blast2Sequences https://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html
BLAT http://genome.ucsc.edu/cgi-bin/hgBlat
ClustalW https://www.ebi.ac.uk/Tools/msa/
DIALIGN2 https://bibiserv.cebitec.uni-bielefeld.de/dialign/
EMBOSS https://www.ebi.ac.uk/Tools/emboss/
GLASS http://glass.lcs.mit.edu/
LAGAN http://lagan.stanford.edu/lagan_web/index.shtml
LALIGN http://www.ch.embnet.org/software/LALIGN_form.html
MUMmer http://mummer.sourceforge.net
Pattern Hunter https://www.bioinfor.com/peaks-software/
Pfam http://pfam.xfam.org
PipMaker http://pipmaker.bx.psu.edu/pipmaker/
SAM https://compbio.soe.ucsc.edu/sam.html
SSAHA https://www.sanger.ac.uk/resources/software/ssaha2/
SSEARCH http://www.biology.wustl.edu/gcg/ssearch.html
SynPlot https://hscl.cimr.cam.ac.uk/syn_plot_background.html
Tcoffee http://tcoffee.vital-it.ch/apps/tcoffee/index.html
VISTA http://www-gsd.lbl.gov/VISTA/index.html
WUBlast2 https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Job+Dispatcher+Sequence+Analysis+Tools+Home

Clustering of Motifs upstream of Coexpressed Genes from Microarray Data

Clustering of Motifs upstream of Coexpressed Genes from Microarray Data

BioProspector http://bioprospector.stanford.edu/
CREME https://creme.dcode.org/

Clustering of TFBS or Motifs

Clustering of TFBS or Motifs

Cister https://zlab.bu.edu/~mfrith/cister.shtml
GALA https://globin.bx.psu.edu/
RVISTA https://rvista.dcode.org/
TraFaC https://trafac.cchmc.org/trafac/index.jsp

Genetic Resources/Tools

Genetic Resources/Tools

Genome Databases and Browsers

Genome Databases and Browsers

BDGP http://www.fruitfly.org/
Ensembl http://www.ensembl.org/
ExoFish http://www.genoscope.cns.fr/externe/tetraodon/
FlyBase http://rice.bio.indiana.edu:7082/
GRAMENE http://www.gramene.org/
HGSC_Baylor https://www.hgsc.bcm.edu/
JGI https://genome.jgi.doe.gov/portal/
MGD http://www.informatics.jax.org/
NCBI https://www.ncbi.nlm.nih.gov/
NISC http://www.nisc.nih.gov/
Rat Genome http://www.rgd.mcw.edu/
Sanger https://www.sanger.ac.uk/
SGD http://genome-www.stanford.edu/Saccharomyces/
TAIR https://www.arabidopsis.org/
UCSC http://www.genome.ucsc.edu/
Wormbase https://wormbase.org//

Genome Evolutionary Comparative Analysis Tools

Genome Evolutionary Comparative Analysis Tools

Name URL Genomic Sequences from
ECR Browser https://ecrbrowser.dcode.org/ human/mouse/fugu
GALA https://globin.bx.psu.edu/ human/mouse
UCSC http://www.genome.ucsc.edu/ human/mouse/rat
VISTA http://pipeline.lbl.gov/ human/mouse/rat

Molecular Biology

Molecular Biology

ORF https://www.ncbi.nlm.nih.gov/gorf/gorf.html
Reverse Complement http://bioinformatics.org/sms/rev_comp.html
Restriction Enzymes (NEBcutter2) http://tools.neb.com/NEBcutter2/index.php
EST Assembler http://www.bioinformatics.org/zest/

Pattern Finding

Pattern Finding

ANN-Spec http://www.cbs.dtu.dk/services/DNAarray/ann-spec.html
MEME

http://meme.sdsc.edu/meme4_4_0/intro.html

Phylogenetic Footprinting

Phylogenetic Footprinting

FootPrinter http://bio.cs.washington.edu/footprinter
EShadow https://eshadow.dcode.org/

Primer Design

Primer Design

CODEHOP (degenerate primers) https://bio.tools/codehop
Primer3 https://bioinfo.ut.ee/primer3-0.4.0/primer3/
Primer3Plus http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
PrimerX (mutagenic primers) http://bioinformatics.org/primerx/

Transcription Factor Binding Site Analysis

Transcription Factor Binding Site Analysis

CONSITE http://consite.genereg.net
RVISTA https://rvista.dcode.org/
TESS http://www.cbil.upenn.edu/tess/
TRANSFAC https://digitalinsights.qiagen.com/