Bioinformatics Tools – Helix Biogen Institute

Bioinformatics Tools

The shortlisted items in their categories below are links to online tools that are designed for extracting the meaningful information from the mass of molecular biology / biological databases & to carry out sequence or structural analysis.

NCBI (https://www.ncbi.nlm.nih.gov/)
ENA (https://www.ebi.ac.uk/ena/browser/home)
EMBL (https://www.ebi.ac.uk/)
DDBJ (https://www.ddbj.nig.ac.jp/index-e.html)
PlasmodiumDB (https://plasmodb.org/plasmo/app)
GISAID (https://www.gisaid.org/)

PathogenFinder (https://cge.cbs.dtu.dk/services/PathogenFinder/)
Resfinder (https://cge.cbs.dtu.dk//services/ResFinder/)
KmerResistance (https://cge.cbs.dtu.dk/services/KmerResistance-2.2/)
SRST2 (https://github.com/katholt/srst2)
CARD (https://card.mcmaster.ca/home)https://www.gisaid.org/)

Kraken (https://ccb.jhu.edu/software/kraken)
MetaPhlAn2 (https://bitbucket.org/biobakery/metaphlan2)
KmerFinder (https://cge.cbs.dtu.dk/services/KmerFinder/)
QIIME (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249058/)
UPARSE (http://www.ncbi.nlm.nih.gov/pubmed/23955772)
MOTHUR (http://www.ncbi.nlm.nih.gov/pubmed/19801464)
DADA2 (http://www.ncbi.nlm.nih.gov/pubmed/27214047)
MED (http://www.nature.com/ismej/journal/v9/n4/full/ismej2014195a.html)
CLARK (http://www.ncbi.nlm.nih.gov/pubmed/25879410)
FOCUS (http://www.ncbi.nlm.nih.gov/pubmed/24949242)
SUPER-FOCUS (http://www.ncbi.nlm.nih.gov/pubmed/26454280)
MG-RAST (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2563014/)
StrainPhlAn (https://www.ncbi.nlm.nih.gov/pubmed/28167665)
PanPhlan (http://www.ncbi.nlm.nih.gov/pubmed/26999001)
Constrains (http://www.ncbi.nlm.nih.gov/pubmed/26344404)
Sigma (http://www.ncbi.nlm.nih.gov/pubmed/25266224)
LSA (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720164)
Leimena-2013 (https://www.ncbi.nlm.nih.gov/pubmed/23915218)
MetaTrans (https://www.ncbi.nlm.nih.gov/pubmed/27211518)
SAMSA (https://www.ncbi.nlm.nih.gov/pubmed/27687690)

Immunoinformatics

NetCTL (https://services.healthtech.dtu.dk/service.php?NetCTL-1.2)
BCpred server (http://ailab-projects1.ist.psu.edu:8080/bcpred/predict.html)
IEDB (https://www.iedb.org/)
Vaxijen (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html)
ANTIGENpro (http://scratch.proteomics.ics.uci.edu/)
ExPasyProtparam (https://web.expasy.org/protparam/)
Prosa-web (https://prosa.services.came.sbg.ac.at/prosa.php)
GalaxyRefine (https://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE)
AllerTOP (https://www.ddg-pharmfac.net/AllerTOP/)
AllergenFP 1.0 server (http://ddg-pharmfac.net/AllergenFp/)
ToxinPred (http://crdd.osdd.net/raghava/toxinpred/)
iBCE-EL server (http://www.thegleelab.org/iBCE-EL/)
SOPMA server (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html)
ElliPro Server (http://tools.iedb.org/ellipro)
iMOD server (iMODS) (http://imods.chaconlab.org)
C-ImmSim online server (https://kraken.iac.rm.cnr.it/C-IMMSIM/index.php?page=1)

New Generation Sequencing

BLAT (http://genome.ucsc.edu/FAQ/FAQblat.html)
Bowtie (http://bowtie-bio.sourceforge.net)
PATRIC (https://www.patricbrc.org/)

Haddock (https://wenmr.science.uu.nl/#:~:text=HADDOCK%20is%20an%20integrative%20platform,small%20molecules%20and%20nucleic%20acids.)
iGEM Docking (http://gemdock.life.nctu.edu.tw/igemdock.php)
ClusPro 2.0 server (https://cluspro.org/signup.php)
FireDock (https://bioinfo3d.cs.tau.ac.il/FireDock/php.php)
HDock (http://hdock.phys.hust.edu.cn/)

Structural Biology

SWISS-MODEL (https://swissmodel.expasy.org/interactive)
I-TASSER (https://zhanggroup.org/I-TASSER/)
RaptorX (http://raptorx.uchicago.edu/ContactMap/)
Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index)
Scratch Protein (http://scratch.proteomics.ics.uci.edu/)
PDB (https://www.rcsb.org/)