Bioinformatics tools

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 every year: NAR Web Server papers

Pairwise sequence alignment

  • Dotlet – The Java based web server for the comparison of DNA and protein sequences using the dot plot approach, maintained by Swiss Institute of Bioinformatics.
  • Dotplot examples – Learn by examples for the dotplot tool.
  • Align – The web server for the pairwise sequence alignment, maintained by EBI. Either global (Needle) or local (Water) alignment can be performed.

Multiple sequence alignment

  • COLBAT – NCBI Constraint-based Multiple Alignment Tool.
  • Clustal Omega Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.
  • Muscle – The web server for the multiple sequence comparison by log-expectation, maintained at EBI. It claimed to achieve better accuracy with higher speed than ClustalW depending on the chosen options.
  • MAFAT – The web server of high speed multiple sequence alignment using fast fourier transformation, maintained at EBI.
  • KALIGN – The web server of fast and accurate multiple sequence alignment, maintained at EBI.
  • T-Coffe – The web server of several tools for computing, evaluating and manipulating multiple alignments of DNA and protein sequences and structures, developed and maintained by Cedric Notredame at Center for Genomic Regulation, Spain.
  • Weblogo – The web server for the generation of sequence logos, developed and maintained by University of California at Berkeley.
  • Skylign – The web server for the generation of HMM logos.

Sequence similarity search

  • NCBI BLAST – 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 different genomes.
  • EBI Sequence Similarity Seacrh – The entry page of the EBI sequence similarity search including FASTA, BLAST and SSEARCH, GGSearch, GLSearch.
  • Sanger BLAST – The entry page of the sequence projects BLAST search services at the Sanger Institute, featured with the special genome databases generated by the completed or ongoing sequencing projects.
  • Ensembl BLAST/BLAT – The BLAST and BLAT search tool implemented in the Ensembl platform.
  • UCSC BLAT – The web server for the genome database search, integrated in the UCSC genome browser platform.
  • HMMER Search – 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 pariwise sequence alignment and multiple sequence alignment.
  • EBI EMBOSS tools – The entry page for the EBI EMBOSS tools.
  • EMBOSS Explorer – The EMBOSS user interface maintained by the Bioinformatics Center at the Netherlands.
  • WebLab – The comprehensive and user-friendly bioinformatics platform developed by the Center for Bioinformatics, Peking University. WebLab provides user spaces to store and manager input data and analysis results.
  • Pasteur Galaxy – The Galaxy server developed by the Pasteur Institute in France.
  • MicroBio Cloud – The EMBOSS tools integrated by the Computer Network Information Center, Chinese Academy of Sciences.

Bioinformatics packages to be downloaded and installed locally

  • EMBOSS – The main portal for the open source bioinformatics project EMBOSS headed by Peter Rice and Alan Bleasby at EBI. EMBOSS is comprehensive package with some 200 individual programs for DNA and protein sequence analysis.
  • InterProScan – The software tool for identification of protein family and domain based-on the integrated database of InterPro.
  • HMMER – The web page for the HMMER package which uses profile hidden Markov models to detect conserved domains in protein sequences, developed and maintained by Sean Eddy at Howard Hughes Medical Institute.
  • Phylogeny software – The whole list of phylogeny programs collected and classified in groups by Joe Felsenstein.

Primer Design

  • Primer Design – The online primer design tool at BioWeb.
  • Primer Blast – NCBI primer design tool with Blast search.
  • Web Primer – Online primer design tool at the yeast genome database.

Motif finding

  • SMART – The web server at EMBL to search known motifs in a protein sequence.
  • MEME – Motif-based sequence analysis tools.
  • InterPro – Protein domain classification at EBI.
  • TMHMM – The web server for the prediction of transmembrane helices in proteins, developed and maintained by Denmark Technical University.

Gene identification

  • FGeneSh – The web server for gene prediction, limited free use for academic users.
  • AUGUSTUS – The web interface for gene prediction at the Bioinformatics Group of the Institute for Mathematics and Computer Science of the University of Greifswald, Germany.
  • GenScan – The web server for the identification of complete gene structures in genomic DNA, maintained by MIT.
  • GenID – The web server o predict genes in anonymous genomic sequences, developed and maintained by University of Pompeu Fabra, Spain.
  • HMMGene – The web server for the prediction of vertebrate and C elegans genes, developed and maintained by the Denmark Technical University.
  • GSDS – The Gene Structure Display Server maintained by the Center of Bioinformatics, Peking Universi.

Protein Interaction

  • STRING – Simlpe name for Search Tool for the Retrieval of Interacting Genes/Proteins, a web servwe to seacrh Known and Predicted Protein-Protein Interactions being maintained at the European Molecular Biology Laboratory, Heidelberg.
  • STITCH – Simlpe name for Search Tool for Interactions of Chemicals, a web servwe to seacrh Chemical-Protein Interactions being maintained at the European Molecular Biology Laboratory, Heidelberg.

Protein sequence analysis and function prediction

  • PredictProtein – A comprehensive web server for the prediction of protein structure and function including secondary structure, protein localization, disorder, disulfide bridges, etc.
  • ProtScale – Display protein sequence profiles as two-dimensional plot calculated based-on predefined amino acid indices including hydrophobicity, secondar structure, accessbility, flexibility, polarity, trasmembrane tendency, etc.

Molecular pylogeney

  • MEGA – The web site for the Molecular Evolutionary Genetics Analysis package developed and maintained by Masatoshi Nei and his colleagues.]
  • Phylip – The web site for the comprehensive package Phylogeny Inference Package (Phylip) created and maintained by Joe Felsenstein at the University of Washington.
  • Tree-Puzzle – The web page for the phylogeny program which uses the maximum likelihood method to analogize nucleotide and amino acid sequences as well as other two-state data.
  • PAML – The web site for the Phylogenetic Analysis by Maximum Likelihood package developed and maintained by Ziheng Yang, at University College, London.
  • DAMBE – The web site for the software package Data Analysis and Molecular Biology and Evolution developed by Xuehua Xia at University of Ottawa, Canada.
  • iTOL – The web site of Interactive Tree of Life for the display and manipulation of phylogenetic trees, developed and maintained by the European Molecular Biology Laboratory.

3D visualization

  • Swiss-PDB Viewer – A comprehensive molecular visualization and modeling package developed by Nicolas Guex at GlaxoSmithKline. It provides a graphical interface and a user friendly control panel for users to analyze several proteins at the same time. There are lots useful functions such as superimposition, mutation and energy minimization for simple molecular simulations.
  • Chimera – UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. High-quality images and animations can be generated. Chimera includes complete documentation and is free of charge for academic, government, nonprofit, and personal use.
  • PyMol – The home page of the molecular visualization system and the useful help information at PyMolWiki.
  • VMD – VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies Reality Application – a comprehensive packge for molecular modeling. The visualization package YASARA View is free for donwloading.
  • YASARA – Yet Another Scientific Artifical Reality Application – a comprehensive packge for molecular modeling. The visualization package YASARA View is free for donwloading.
  • Cn3D – The web page of the molecular visualization program Cn3D developed and distributed by NCBI. It can be installed on your PC to display the three-dimensional structures obtained from the NCBI MMDB database.
  • Kinemage – The home page of the protein visualization package Kinemage developed and maintained at the laboratory of Jane Richardson and David Richardson, Duke University.
  • RasMol – The home page of molecular visualization freeware RasMol, maintained by University of Massachusetts Amherst.

Protein modeling

  • Phyre2 – The web server of Protein Homology/analogY Recognition Engine V2.0 developed and maintained by Imrerial College, UK. Paper CEA
  • Swiss Model – The home page of the automated comparative protein modeling server, hosted by University of Basel and the Swiss Institute of Bioinformatics. Extensive documentation and help materials are provided.
  • SwisDock – A web service to predict the molecular interactions between a target protein and a small molecule, and a database of target and ligand structures.
  • AutoDock – The web site for protein/protein and protein/ligand docking at Scripps Institute.
  • CASP – The entry page for the international protein structure prediction center, hosted at University of California at Davies. It provides the means of objective testing of evaluation of different methods in protein structure prediction.

RNA tools

  • MFOLD – The web server for the prediction of RNA secondary structure, developed and maintained by Michael Zuker at Rensselaer Polytechnic Institute.
  • RAIN – The web server for RNA-protein Asociation and Interaction Netwroks, developed by the Danish Center for Nocoding RNA (RTH).
  • FoldAlign – The web server for RNA structure and sequence aligment, develped by the Danish Center for Noncoding RNA (RTH).
  • RNASNP – The web server for predicting SNP effects on local RNA secondary structure, develped by the Danish Center for Noncoding RNA (RTH).
  • RILogo – 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

  • ExPASy tools – A comprehensive list of online web-based bioinformatics tools provided by ExPASy and worldwide.
  • Tsinghua – List of software tools devloped by the Bioinformatics Division, Tsinghua University.
  • DTU HeathTech Services – The entry page for the bioinformatics tools at the Department of Health Technology, the Technical University of Denmark.
  • SMS – Sequence manipulation suite at Bioinformatics.org.
  • Omics Tools – OMICtools is a workflow for omics data analysis. All tools have been classified by omic technologies (NGS, microarray, PCR, MS, NMR), applications and analytical steps.
  • GoGe – The platform for Gomparative Genomics.
Scroll to Top