There are many bioinformatics tools over the Internet.
Thanks to the great
contribution of the scientific community of bioinformatics research and
development. They make the bioinformatics programs and packages freely
available to the end user biologists. The web-based tools can be accessed
through the Internet using the web browsers. Users may also download and
install some of the packages on a local machine to run the programs.
The journal Nucleic Acids Research publishes a special Web Service issue
NAR Web Server papers
Pairwise sequence alignment
- Needleman-Wunsch global sequence alignment at EBI.
- Needleman-Wunsch global sequence alignment at NCBI.
- Pairwise structure and sequence alignment at PDB.
- Smith-Waterman local sequence alignment at EBI.
- Align two or more sequences using BLAST at NCBI.
- Sequence comparison with dot plot at SIB.
Multiple sequence alignment
- NCBI Constraint-based Multiple Alignment Tool.
Clustal Omega is a new multiple sequence alignment program that uses
seeded guide trees and HMM profile-profile techniques to generate alignments.
- Multiple sequence comparison with better accuracy and higher speed.
- High speed multiple sequence alignment using fast fourier transformation,
- The web server of fast and accurate multiple sequence alignment at EBI.
- Multiple alignments of DNA and protein sequences and structures, at Center
for Genomic Regulation, Spain.
Sequence similarity search
- The central point of the NCBI BLAST server which provides whole functionality
of DNA and protein sequence database search programs including PSI-BLAST
and PHI-BLAST, and the whole list of databases in different scales and
- The BLAST tool at Beijing Institute of Genomics.
EBI Sequence Similarity Seacrh
- EBI sequence similarity search including FASTA,
BLAST and SSEARCH, GGSearch, GLSearch.
- BLAST search services at the Sanger
Institute, with special genome databases generated by the
completed or ongoing sequencing projects.
- The BLAST and BLAT search tool implemented in the Ensembl platform.
- The web server for the genome database search, integrated in the UCSC genome
- Sequence profile Hidden Markov Model (HMMER) server developed and maintained by EBI.
Web-based bioinformatics platforms
NCBI BLAST tools
- The BLAST platform at NCBI with many tools including Needleman-Wunsch
global pairwise sequence alignment and multiple sequence alignment.
EBI EMBOSS tools
- The entry page for the EBI EMBOSS tools.
- The EMBOSS user interface maintained by the Bioinformatics Center at the
- The Sequence analysis platform developed by the Center for Bioinformatics (CBI),
Bioinformatics packages to be downloaded and installed locally
- The main portal for the open source bioinformatics project EMBOSS.
- Identification of protein family and domain based-on the
integrated database of InterPro.
- Profile hidden Markov models to detect conserved domains in protein sequences.
- The whole list of phylogeny programs collected and classified
in groups by Joe Felsenstein.
Protein sequence analysis and function prediction
- Computating various physical and chemical parameters for a protein sequence,
including the molecular weight, theoretical pI, amino acid composition,
- Display protein sequence profiles as two-dimensional plot, including hydrophobicity, secondary structure, accessibility, flexibility, polarity, transmembrane tendency, etc.
- Prediction of protein function including secondary structure, protein localization, disorder, disulfide bridges, etc.
- The web server for the generation of sequence logos, developed and maintained
by University of California at Berkeley.
- The web server at EMBL to search known motifs in a protein sequence.
- Motif-based sequence analysis tools.
- Protein domain classification at EBI.
- Prediction of signal peptide at Denmark Technical University.
- Prediction of transmembrane helices at Denmark Technical University.
- The online primer design tool at BioWeb.
- NCBI primer design tool with Blast search.
- Online primer design tool at the yeast genome database.
- The web server for gene prediction, limited free use for academic users.
- Gene prediction tool at the University of Greifswald, Germany.
- The web server for the identification of complete gene structures in genomic
DNA at MIT.
- The web server for the prediction of vertebrate and C elegans genes,
developed and maintained by the Denmark Technical University.
- The Gene Structure Display Server maintained by the Center of Bioinformatics, Peking Universi.
- Molecular Evolutionary Genetics Analysis package.
- Phylogeny Inference Package created by Joe Felsenstein at the University of
Phylogenetic Analysis by Maximum Likelihood package
developed and maintained by Ziheng Yang, at University College, London.
- Data Analysis and Molecular Biology and Evolution developed by Xuehua Xia at University of Ottawa, Canada.
- Interactive Tree of Life, for the display and manipulation of phylogenetic trees.
- Interactive visualization and analysis of 3D structures at UCSF.
- A comprehensive molecular visualization and modeling package at SIB.
- The home page of the molecular visualization system and the useful help
information at PyMolWiki.
- Modeling, visualization, and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies.
- The home page of molecular visualization freeware RasMol, maintained by
University of Massachusetts Amherst.
- Automated comparative protein modeling server at SIB.
- Protein Homology/analogY Recognition Engine at Imrerial College, UK.
- Prediction of molecular interactions between a target protein and a
- The web site for protein/protein and protein/ligand docking at
- The international protein structure prediction center.
- The UNAFold web server for mfold & DINAMelt.
- The web server for RNA-protein Asociation and Interaction Netwroks, developed by the Danish Center for Nocoding RNA (RTH).
- The web server for RNA structure and sequence alignment, developed by the
Danish Center for Noncoding RNA (RTH).
- The web server for predicting SNP effects on local RNA secondary structure,
develped by the Danish Center for Noncoding RNA (RTH).
- The web server for creating RNA-RNA interaction logos for two RNAs,
developed by the Danish Center for Noncoding RNA (RTH).
List of bioinformatics tools at international bioinformatics centers
- A comprehensive list of online web-based bioinformatics tools provided
by ExPASy and worldwide.
- List of software tools developed by the Bioinformatics Division, Tsinghua
DTU HeathTech Services
- The entry page for the bioinformatics tools at the Department of Health
Technology, the Technical University of Denmark.
- Sequence manipulation suite at Bioinformatics.org.
- The platform for Gomparative Genomics.
- Online tools integrated by the Softberry bioinformatics company in US.
4 June 2023,
, Beijing, China