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.
- DDBJ (https://www.ddbj.nig.ac.jp/index-e.html)
- EMBL (https://www.ebi.ac.uk/)
- ENA (https://www.ebi.ac.uk/ena/browser/home)
- GISAID (https://www.gisaid.org/)
- HBVdb
- NCBI (https://www.ncbi.nlm.nih.gov/)
- PlasmodiumDB (https://plasmodb.org/plasmo/app)
- VEuPathDB
- Virus Pathogen Database and Analysis Resource (ViPR)
- 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/)
- CARD (https://card.mcmaster.ca/home)https://www.gisaid.org/)
- Codon Usage Database
- iTOL
- KEGG: Kyoto Encyclopedia of Genes and Genomes
- KmerResistance (https://cge.cbs.dtu.dk/services/KmerResistance-2.2/)
- MAFFT - a multiple sequence alignment program
- MLST
- PathogenFinder (https://cge.cbs.dtu.dk/services/PathogenFinder/)
- PubMLST
- RAPT - NCBI
- Resfinder (https://cge.cbs.dtu.dk//services/ResFinder/)
- SRST2 (https://github.com/katholt/srst2)
- VirulenceFinder
- AllergenFP 1.0 server (http://ddg-pharmfac.net/AllergenFp/)
- AllerTOP (https://www.ddg-pharmfac.net/AllerTOP/)
- ANTIGENpro (http://scratch.proteomics.ics.uci.edu/)
- BCEPRED Submission page
- BCpred server (http://ailab-projects1.ist.psu.edu:8080/bcpred/predict.html)
- C-ImmSim online server (https://kraken.iac.rm.cnr.it/C-IMMSIM/index.php?page=1)
- ElliPro Server (http://tools.iedb.org/ellipro)
- ExPASy - ProtParam tool
- ExPasyProtparam (https://web.expasy.org/protparam/)
- GalaxyRefine (https://galaxy.seoklab.org/cgi-bin/submit.cgi?type=REFINE)
- iBCE-EL server (http://www.thegleelab.org/iBCE-EL/)
- IEDB (https://www.iedb.org/)
- iMOD server (iMODS) (http://imods.chaconlab.org)
- NetCTL (https://services.healthtech.dtu.dk/service.php?NetCTL-1.2)
- NPS@ : SOPMA secondary structure prediction
- ProSA-web - Protein Structure Analysis
- Prosa-web (https://prosa.services.came.sbg.ac.at/prosa.php)
- Scratch Protein Predictor
- SOPMA server (https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html)
- ToxinPred (http://crdd.osdd.net/raghava/toxinpred/)
- Vaxijen (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html)
- CLARK (http://www.ncbi.nlm.nih.gov/pubmed/25879410)
- Constrains (http://www.ncbi.nlm.nih.gov/pubmed/26344404)
- DADA2 (http://www.ncbi.nlm.nih.gov/pubmed/27214047)
- FOCUS (http://www.ncbi.nlm.nih.gov/pubmed/24949242)
- kbase
- KmerFinder
- KmerFinder (https://cge.cbs.dtu.dk/services/KmerFinder/)
- Kraken (https://ccb.jhu.edu/software/kraken)
- Leimena-2013 (https://www.ncbi.nlm.nih.gov/pubmed/23915218)
- LSA (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720164)
- MED (http://www.nature.com/ismej/journal/v9/n4/full/ismej2014195a.html)
- MetaPhlAn2 (https://bitbucket.org/biobakery/metaphlan2)
- MetaTrans (https://www.ncbi.nlm.nih.gov/pubmed/27211518)
- MG-RAST (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2563014/)
- MOTHUR (http://www.ncbi.nlm.nih.gov/pubmed/19801464)
- PanPhlan (http://www.ncbi.nlm.nih.gov/pubmed/26999001)
- QIIME (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3249058/)
- SAMSA (https://www.ncbi.nlm.nih.gov/pubmed/27687690)
- Sigma (http://www.ncbi.nlm.nih.gov/pubmed/25266224)
- StrainPhlAn (https://www.ncbi.nlm.nih.gov/pubmed/28167665)
- SUPER-FOCUS (http://www.ncbi.nlm.nih.gov/pubmed/26454280)
- UPARSE (http://www.ncbi.nlm.nih.gov/pubmed/23955772)
- org
- ipynb - Colaboratory
- I-TASSER (https://zhanggroup.org/I-TASSER/)
- PDB (https://www.rcsb.org/)
- Phyre2 (http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index)
- RaptorX (http://raptorx.uchicago.edu/ContactMap/)
- RCSB PDB
- Scratch Protein (http://scratch.proteomics.ics.uci.edu/)
- SWISS-MODEL (https://swissmodel.expasy.org/interactive)
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