Sequence Analysis Tools
Pairwise Sequence Alignment Tools
Basic Local Alignment Search Tool (BLAST) : https://blast.ncbi.nlm.nih.gov/Blast.cgi (Alignment and Similarity Searching)
Multiple Sequence Alignment Tools
Clustal Omega: https://www.ebi.ac.uk/jdispatcher/msa/clustalo
Clustal W: https://www.genome.jp/tools-bin/clustalw
MAFFT : https://mafft.cbrc.jp/alignment/software/
Sequence Analysis Tools
Ensemble: https://asia.ensembl.org/index.html (Exon, Intron, Genomic Content)
UniProt: https://www.uniprot.org/ (Functional domains, variants, PTMs)
Motif Based Sequence Analysis Tool
MEME : https://meme-suite.org/meme/
Mutation and Cancer Analysis
COSMIC : https://cancer.sanger.ac.uk/cosmic/
cBioPortal : https://www.cbioportal.org/
Protein Protein Interactions
STRING : https://string-db.org/
BioGRID : https://thebiogrid.org/
IntAct : https://www.ebi.ac.uk/intact/home
Protein Parameter (Physiochemical) Calculator
ProtParam : https://web.expasy.org/protparam/
GPCR Protein : https://gpcr.utep.edu/
Gene Expression Profiling
GTEx : https://www.gtexportal.org/home/
GEO Profiles : https://www.ncbi.nlm.nih.gov/geoprofiles/
Target Prediction
miRTarBase : https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/index.php miRNA Targetting
TargetScan : https://www.targetscan.org/vert_80/
Structural Biology
SwissModel : https://swissmodel.expasy.org/interactive
I-TASSER : https://zhanggroup.org/I-TASSER/ Protein structure and function prediction
Disease Pathway
Kegg Pathway : https://www.genome.jp/kegg/pathway.html
Biocarta :
Open Reading Frame Finder
ORF Finder: https://www.ncbi.nlm.nih.gov/orffinder/
Transcription/Translation
Expasy Translate: https://web.expasy.org/translate/ (DNA/RNA to Protein)
Structural Bioinformatics & Molecular Modeling
PyMOL: https://pymol.org/
Avogadro: https://avogadro.cc/
Molecular Docking
AutoDock: https://autodock.scripps.edu/ (MGLTools required to work on GUI)
MGLTools: https://ccsb.scripps.edu/mgltools/downloads/
SwissDock : https://www.swissdock.ch/ (Online Tools)
Chimera : https://www.cgl.ucsf.edu/chimera/download.html
I-TASSER : https://zhanggroup.org/I-TASSER/
DockThor: https://dockthor.lncc.br/v2/
CASTpFold : https://cfold.bme.uic.edu/castpfold/ Active Site Prediction in Protein Before Docking
Virtual Screening
SwissADME: http://www.swissadme.ch/
Phylogenetics
MEGA (Molecular Evolutionary Genetics Analysis): https://www.megasoftware.net/
IQ-TREE: http://www.iqtree.org/
iTOL: https://itol.embl.de/itol.cgi
Primer Design
PrimerBLAST: https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Primer3Web: https://primer3.ut.ee/
OligoAnalyzer: https://sg.idtdna.com/calc/analyzer (Create Account at First)
Drug Discovery
Therapeutic Target Database: https://ttd.idrblab.cn/
OrthoVenn2 : https://orthovenn2.bioinfotoolkits.net/
Database of Essential Genes (DEG) : http://origin.tubic.org/deg/public/index.php
Gene Prediction Tools
Online Tools
GENSCAN: http://hollywood.mit.edu/GENSCAN.html
Augustus: https://bioinf.uni-greifswald.de/augustus/submission.php
GeneMark: https://exon.gatech.edu/
Offline Tools
GENSCAN: http://hollywood.mit.edu/gendist.html
Augustus: https://bioinf.uni-greifswald.de/augustus/downloads/
EuGene: http://eugene.toulouse.inra.fr/