Applied Bioinformatics Course [中文]

Pairwise sequence alignment

• Needle - EBI Needleman-Wunsch global sequence alignment.
• Water - EBI Smith-Waterman local sequence alignment.
• Global Align - NCBI Needleman-Wunsch global sequence alignment.
• Stucture Alignment - PDB pairwise structure and sequence alignment.
• Dottup - EBI Dot plot for DNA sequences.
• Dotmatcher - EBI Dot plot for protein sequences only.
• Blast2Seq - Align two or more sequences using BLAST at NCBI.
• Dotlet - Sequence comparison with dot plot at SIB. Examples

Multiple sequence alignment

• COBALT - 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 - Multiple sequence comparison with better accuracy and higher speed.
• MAFAT - High speed multiple sequence alignment using fast fourier transformation, at EBI.
• KALIGN - The web server of fast and accurate multiple sequence alignment at EBI.
• T-Coffe - Multiple alignments of DNA and protein sequences and structures, at Center for Genomic Regulation, Spain.

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.
• BIGD BLAST - The BLAST tool at Beijing Institute of Genomics.
• EBI Sequence Similarity Seacrh - EBI sequence similarity search including FASTA, BLAST and SSEARCH, GGSearch, GLSearch.
• Sanger BLAST - BLAST search services at the Sanger Institute, with 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 pairwise 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 Sequence analysis platform developed by the Center for Bioinformatics (CBI), Peking University.

Bioinformatics packages to be downloaded and installed locally

• EMBOSS - The main portal for the open source bioinformatics project EMBOSS.
• InterProScan - Identification of protein family and domain based-on the integrated database of InterPro.
• HMMER - Profile hidden Markov models to detect conserved domains in protein sequences.
• Phylogeny software - The whole list of phylogeny programs collected and classified in groups by Joe Felsenstein.

Protein sequence analysis and function prediction

• ProtParam - Computating various physical and chemical parameters for a protein sequence, including the molecular weight, theoretical pI, amino acid composition, atomic composition.
• ProtScale - Display protein sequence profiles as two-dimensional plot, including hydrophobicity, secondary structure, accessibility, flexibility, polarity, transmembrane tendency, etc.
• PredictProtein - Prediction of protein function including secondary structure, protein localization, disorder, disulfide bridges, etc.

Motif finding

• Weblogo - The web server for the generation of sequence logos, developed and maintained by University of California at Berkeley.
• 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.
• SignalP - Prediction of signal peptide at Denmark Technical University.
• TMHMM - Prediction of transmembrane helices at Denmark Technical University.

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.

Gene identification

• FGeneSh - The web server for gene prediction, limited free use for academic users.
• AUGUSTUS - Gene prediction tool at the University of Greifswald, Germany.
• GenScan - The web server for the identification of complete gene structures in genomic DNA at MIT.
• 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.

Molecular phylogeny

• MEGA - Molecular Evolutionary Genetics Analysis package.
• Phylip - Phylogeny Inference Package created by Joe Felsenstein at the University of Washington.
• PAML - Phylogenetic Analysis by Maximum Likelihood package developed and maintained by Ziheng Yang, at University College, London.
• DAMBE - Data Analysis and Molecular Biology and Evolution developed by Xuehua Xia at University of Ottawa, Canada.
• iTOL - Interactive Tree of Life, for the display and manipulation of phylogenetic trees.

3D visualization

• ChimeraX - Interactive visualization and analysis of 3D structures at UCSF.
• Swiss-PDB Viewer - A comprehensive molecular visualization and modeling package at SIB.
• PyMol - The home page of the molecular visualization system and the useful help information at PyMolWiki.
• VMD - Modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies.
• RasMol - The home page of molecular visualization freeware RasMol, maintained by University of Massachusetts Amherst.

Protein modeling

• Swiss Model - Automated comparative protein modeling server at SIB.
• Phyre - Protein Homology/analogY Recognition Engine at Imrerial College, UK. Paper
• SwisDock - Prediction of molecular interactions between a target protein and a small molecule.
• AutoDock - The web site for protein/protein and protein/ligand docking at Scripps Institute.
• CASP - The international protein structure prediction center.

RNA tools

• UNAFOLD - The UNAFold web server for mfold & DINAMelt.
• 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 alignment, developed 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.
• 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.
• CoGe - The platform for Comparative Genomics.
• Softberry - Online tools integrated by the Softberry bioinformatics company in US.