Bioinformatics Resources
A list of resources related to molecular genetics and phylogeny.
Page last updated: 24th March 2001
| Genetic Future | Self-linking mayhem. |
| General Bioinformatics Resources | Links to sequence analysis tutorials and major bioinformatics organisations. |
| Phylogeny | Online phylogenies, information on phylogenetic reconstruction, and software for making and viewing phylogenetic trees. |
| Genomics | Organisations, databases and other resources related to genomic analysis. |
| Sequence Databases | Online collections of molecular data, including protein and nucleotide sequences and structural information. |
| Analysis Tools | Tools for finding, aligning and comparing sequences, finding and translating genes, and predicting protein structure. |
| Metabolic Pathways | Resources related to metabolic enzymes and pathways from a variety of species. |
| Developmental Genetics | Information on the developmental processes of different organisms and the genes that control them. |
General Bioinformatics Resources
| Introduction to Biosequence Comparison | A useful summary of the major programs and techniques used for sequence analysis. |
| Bioinformatics and Genomic Analysis | An excellent introduction to bioinformatics from a university course guide. Perfect for newcomers to sequence analysis. |
| The Bioinformatics Resource | The most comprehensive list of bioinformatics resources I've come across, compiled by CCP11. |
| Bioinformatics Resources | A useful list of databases and online tools. |
| NCBI Home Page | Home of the National Center for Biotechnology Information. My favourite bioinformatics site. |
| EBI Home Page | Home of the European Bioinformatics Institute, containing many useful links. |
| ExPASy | The proteomics server of the Swiss Institute of Bioinformatics, containing many sequence analysis resources. |
| National Biotechnology Information Facility | A truly impressive resource for anyone interested in biotechnology. |
| The Tree of Life | A thorough description of our current understanding of the phylogenetic tree. |
| The UCMP Phylogeny Wing | Less thorough than The Tree of Life, but useful for a general overview of phylogenetic relationships. |
| Introduction to Phylogenetic Systematics | A neat introduction to phylogenetic methods by the Society of Australian Systematic Biologists. |
| Introduction to Cladistics | A useful introduction to the best method available for phylogenetic analysis. |
| Glossary of Phylogenetic Systematics | Definitions of the terms used in the study of phylogenetics. |
| Reconstructing Phylogenetic Trees | Summary of the process of phylogeny construction with the aid of a Java applet. |
| Evolutionary and Geological Timelines | A brief history of major evolutionary events, and a table of the geological periods. |
| Species 2000 | A British attempt to index the scientific names of all known species. |
| Computer Programs for Phylogenetic Analysis | For the serious-minded investigator into phylogenetic relationships. |
| Phylogeny Programs | An excellent site that provides links to virtually every available phylogeny package. |
| Phylogenetics Software Resources | A list of software tools for researchers in phylogenetics, provided by the UCMP. |
| TreeBASE | A database of phylogenetic trees and data matrices. |
| TreeView | A relatively simple program for viewing phylogenetic trees, compatible with TreeBASE data and phylogenies. |
| TreeGen | Online tree generation from distance data. |
| PHYLIP Home Page | A free package of programs for inferring phylogenies. |
| PAUP | Phylogenetic Analysis Using Parsimony. Windows version ($85 plus postage) can be ordered through Sinauer Associates. |
| The Institute for Genomic Research | A non-profit sequencing centre created by Craig Venter, with links to microbial genome databases. |
| UCSC Genome Bioinformatics | Interactive interface to the working drafts of the human and mouse genome databases. |
| NCGR Home Page | Home of the National Center for Genome Resources. |
| NCBI Entrez Genomes | Access to publicly available genome sequence data. |
| The Genome Database | An international collaboration supporting the Human Genome Project. |
| Human Genome Project Information | Information on the public project to sequence the human genome. |
| Mouse Genome Informatics | Resources related to the genetics and biology of laboratory rodents. |
| FlyBase | A comprehensive database of the Drosophila genome. |
| COG | Clusters of Orthologous Groups of proteins and their phylogenetic distribution. |
| Database of Genome Sizes | The lengths of genomes from a wide variety of organisms. |
| Entrez |
DNA and protein sequences, 3D structures, genomes and taxonomy. Information on use can be found at Entrez Help. |
| Sequence Retrieval System (SRS) | A network browser for molecular biology databases, run by the EBI. |
| BCM Search Launcher | A collection of online molecular search and analysis services. |
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A database of DNA and RNA sequences submitted directly by researchers. |
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Information on wild-type proteins, including sequences, homology, and functional and structural data. |
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Annotated protein sequence database provided by ExPASy. |
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A database of protein families and domains, allowing assignment of a protein sequence to a known family. |
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An automatic compilation of homologous domains detected in the SWISS-PROT database. |
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A non-redundant protein database organized according to family relationships. |
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Displays the 400 possible packing interactions between pairs of amino acid side chains. |
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The Molecular Modelling Database, a database of macromolecular 3D structures. |
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Three-dimensional structural information on known proteins. |
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Tools for sequence similarity analysis provided by the NCBI. Includes Basic BLAST and PSI-BLAST tools. |
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Sensitive similarity searches using a variety of programs and databases. |
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Multiple sequence alignment for DNA and protein sequences. |
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The ftp download site of the multiple sequence alignment program. The help file can be found here. |
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For sequence searches and comparisons. |
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Sequence similarity and homology searching against nucleotide and protein databases. |
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How to format sequences into FASTA, one of the most widely used search languages. |
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A tool for characterising families of sequences. |
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Splice sites, protein coding exons, gene model construction and promoter recognition. |
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Finds and identifies all open reading frames in a given nucleotide sequence. |
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Translates DNA sequences into proteins. |
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Predicts the secondary structure of a protein from its amino acid sequence. |
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A variety of resources related to protein structure prediction. |
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Free versions of the programs required to view PDB files. |
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Graphical representations of all major metabolic pathways, primarily those important to human biochemistry. |
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Interactive metabolic reconstruction and simulation using information from 39 sequenced genomes. |
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An extensive database of metabolic enzymes and pathways. |
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A searchable index of biochemical pathways. |
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A very useful collection of genomic data, including metabolic genes present in various species. |
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Vital for the interpretation of the COG Database and the KEGG Encyclopedia. |
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A list of links to a variety of educational resources on developmental biology. |
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A database of homeobox genes (including hox genes) from various species. |
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Information on homeobox genes, including classification and evolution. |
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Details of evolutionarily conserved developmental pathways, provided by the The Interactive Fly. |
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Resources related to developmental genetics and biology. |
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A summary of conserved homeobox gene activity, from the University of Virginia. |
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