151

Useful Tools and Web Links

ALGGEN PROMO

https://alggen.lsi.upc.es/cgi-­bin/promo_v3/promo/promoinit.

cgi?dirDB=TF_8.3

AnDOM

https://andom.bioapps.biozentrum.uni-­wuerzburg.de/index_new.

html

BLAST

https://blast.ncbi.nlm.nih.gov/Blast.cgi

CATH

https://www.cathdb.info/

cBioPortal

https://www.cbioportal.org/

DrumPID

https://drumpid.bioapps.biozentrum.uni-­wuerzburg.de/compounds/

index.php

ELM

https://elm.eu.org

EMBL-EBI

https://www.ebi.ac.uk/services

ExPASy

https://www.expasy.org

GENEVESTIGATOR

https://genevestigator.com/gv/

Genomatix

https://www.genomatix.de/

GEO

https://www.ncbi.nlm.gov/geo/

iHOP

https://www.ihop-­net.org/UniPub/iHOP/

iRegulon

https://iregulon.aertslab.org/

I-TASSER

https://zhanglab.ccmb.med.umich.edu/I-­TASSER/

Jimena

https://www.bioinfo.biozentrum.uni-­wuerzburg.de/computing/jimena_c/

KEGG

https://www.genome.jp/kegg/

LOMETS

https://zhanglab.ccmb.med.umich.edu/LOMETS/

MEME Suite

https://meme-­suite.org/

Metatool

https://pinguin.biologie.uni-­jena.de/bioinformatik/networks/

metatool/metatool5.0/metatool5.0.html

miRanda

https://www.microrna.org/microrna/home.do

MUSCLE

https://www.ebi.ac.uk/Tools/msa/muscle/

NCBI

https://www.ncbi.nlm.nih.gov/pubmed/

Nucloc

https://www.nucloc.org/

PDB

https://www.rcsb.org/pdb/home/home.do

Pfam

https://pfam.xfam.org/

PlateletWeb

https://plateletweb.bioapps.biozentrum.uni-­wuerzburg.de/

plateletweb.php

ProDom

https://prodom.prabi.fr/prodom/current/html/home.php

PRODORIC

https://prodoric.tu-­bs.de/

PROSITE

https://prosite.expasy.org

PyMOL

https://www.pymol.org/

QUARK

https://zhanglab.ccmb.med.umich.edu/QUARK/

Ramachandran Plot

https://mordred.bioc.cam.ac.uk/~rapper/rampage.php

RasMol

https://www.openrasmol.org/

Rfam

https://rfam.xfam.org/

RNAAnalyzer

https://rnaanalyzer.bioapps.biozentrum.uni-­wuerzburg.de

RNAfold

https://rna.tbi.univie.ac.at/cgi-­bin/RNAWebSuite/RNAfold.cgi

(continued)

11.3  Exercises for Chap. 11