Links for Online Resources
Chapter 16 Links for On-Line Resources
BLAST
https://blast.ncbi.nlm.nih.gov/Blast.cgi
BLASTN
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
BLASTP & PSI-BLAST
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
BLASTX
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
TBLASTN
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
smartBLAST
https://blast.ncbi.nlm.nih.gov/smartblast/?LINK_LOC=BlastHomeLink
Downloading BLAST
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
Conserved Domain Search
https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
CDART
https://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps
European Molecular Biology Open Software Suite
http://emboss.sourceforge.net/
EMBOSS Water
https://www.ebi.ac.uk/Tools/psa/emboss_water/
EMBOSS Matcher
https://www.ebi.ac.uk/Tools/psa/emboss_matcher/
EMBOSS Needle
https://www.ebi.ac.uk/Tools/psa/emboss_needle/
EMBOSS Stretcher
https://www.ebi.ac.uk/Tools/psa/emboss_stretcher/
Clustal Omega
https://www.ebi.ac.uk/Tools/msa/clustalo/
T-Coffee
https://www.ebi.ac.uk/Tools/msa/tcoffee/
PSORT
https://www.psort.org/
SignalP
http://www.cbs.dtu.dk/services/SignalP/
EMBOSS Peptats
https://www.ebi.ac.uk/Tools/seqstats/emboss_pepstats/
PredictProtein
https://www.predictprotein.org/about
ExPASy
https://www.expasy.org/
Primer3
https://primer3.org/
Primer-BLAST
https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome
NEBcutter
http://nc2.neb.com/NEBcutter2/
Chapter 17 Links for On-Line Resources
Prokaryotic Genomes Automatic Annotation Pipeline (PGAP)
https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
RAST (Rapid Annotation using Subsystem Technology)
http://rast.theseed.org/FIG/rast.cgi
Prokka
http://www.vicbioinformatics.com/software.prokka.shtml
Artemis Genome Browser
https://www.sanger.ac.uk/science/tools/artemis
GenDB
https://www.uni-giessen.de/fbz/fb08/Inst/bioinformatik/software/gendb
OrthoMCL
https://orthomcl.org/orthomcl/
Artemis Comparison Tool
https://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act
BLAST Ring Image Generator (BRIG)
http://brig.sourceforge.net/
Mauve Multiple Genome Alignment
http://darlinglab.org/mauve/mauve.html
Galaxy
https://usegalaxy.org/