356

Programming Languages

Biojava

https://biojava.org/

BioPerl

https://bioperl.org/

C++

https://www.cplusplus.com/

Java

https://www.oracle.com/technetwork/java/index.html

Perl

https://www.perl.org/

Python

https://www.python.org/

R

https://cran.r-­project.org/

Bioconductor

https://www.bioconductor.org/

Promoter Analysis

ALGGEN

PROMO

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

cgi?dirDB=TF_8.3

Genomatix

https://www.genomatix.de/

JASPAR

https://jaspar.genereg.net/cgi-­bin/jaspar_db.pl

MotifMap

https://motifmap.igb.uci.edu/

TESS

https://www.cbil.upenn.edu/tess/

TRANSFAC

https://www.gene-­regulation.com/pub/databases.html

Protein Analysis

AnDom

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

index_new.html

CATH

https://www.cathdb.info/

Conserved Domains

https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

ExPASy

https://www.expasy.org

InterPro

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

MODELLER

https://salilab.org/modeller/tutorial/

PDB

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

Pfam

https://pfam.xfam.org/

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/

SCOP (old)

https://scop.mrc-­lmb.cam.ac.uk/scop/

SCOP updated

https://scop.berkeley.edu/

SMART

https://smart.embl-­heidelberg.de/

Overview of Important Databases and Programs and Their General Use