Databases & Software Systems
Bioinformatics Research Centre, University of Glasgow

Databases

  • RAPAD: RNA and Protein Abundance Database at Glasgow (author: Andy Jones)

  • Database of Small Hydrogen-Bonded Protein Motifs (authors: David Leader and James Milner-White)

  • Topology Of Protein Structure (authors: Ioannis Michalopoulos, Gilleain Torrance, David Gilbert and David Westhead)

    Software

    Grid Software

  • BRIDGES project visualisation tools for synteny and data federation (author: BRIDGES project)

  • BRIDGES GridBLAST - a parallelized BLAST service using grid computing technology (author: BRIDGES project)

    Microarray analysis

  • GlaMA Glasgow Microarray Analysis (authors: Rainer Breitling and Pawel Herzyk)

    Protein sequence analysis

  • MSAT - Multiple Sequence Alignment tool based on TOPS (author: Te Ren)

    Protein structure and function

  • Motivated Proteins: web interface to the Protein Motif database (authors: David Leader and James Milner-White)

  • TOPS motif database and search engine (author: Juris Viksna)

  • Topology-based protein structure comparison and motif matching New, fast, web-server system. (author: Gilleain Torrance)

    Biochemical Networks

  • MetaNetter -- Cytoscape plugin for the inference and visualization of networks from high-resolution mass spectrometry metabolomic data. (author: Fabien Jourdan). Reference: Jourdan F, Breitling R, Barrett M and Gilbert D. MetaNetter: inference and visualization of high-resolution metabolomic networks. (2007) In press Bioinformatics.

  • BioNessie - biochemical pathway simulation and analysis tool. (author: Xuan Liu).

  • BioNessie Lite command-line version of BioNessie biochemical pathway simulation and analysis tool. (author: Robin Donaldson).

  • MC2(PLTLc) - PLTLc model checker. (author: Robin Donaldson).

    Genome visualisation and analysis

  • VisGenome genome map visualisation combining single and comparative views, and providing integrated data from several sources. (authors: Joanna Jakubowska, Ela Hunt, Matthew Chalmers, Martin McBride, and Anna F. Dominiczak)

  • BugView: A desktop browser for viewing and comparing genomes: http://www.gla.ac.uk/~dpl1n/BugView/ Author: David Leader

  • DerBrowser: A java applet for viewing distributed chromosome maps: http://www.gla.ac.uk/~dpl1n/derBrowser/ Author: David Leader

  • Dinucleotide: A program for examining the effect of reading-frame on dinucleotide frequency: http://www.gla.ac.uk/~dpl1n/dinucleotide/ Author: David Leader

    Phylogenetic Trees

    Author: Rod Page

  • TreeView: Tree drawing software for Apple Macintosh and Windows http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

  • COMPONENT: a program for analysing evolutionary trees http://taxonomy.zoology.gla.ac.uk/rod/cpw.html

  • TreeMap: an experimental program for comparing host and parasite trees. http://taxonomy.zoology.gla.ac.uk/rod/treemap.html

  • GeneTree: an experimental program for comparing gene and species trees. http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html

  • Spectrum (TM): program to read in a data file comprising aligned character arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform some simple spectral analysis procedures on that data. http://taxonomy.zoology.gla.ac.uk/~mac/spectrum/spectrum.html

  • NDE (NEXUS Data Editor) is a program to create and edit NEXUS format data files http://taxonomy.zoology.gla.ac.uk/rod/NDE/nde.html