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Resources

The following list contains links to the on-line resources provided by our research group. Should any of the links be broken or for general enquiries please contact: bioinformatics-webmaster@manchester.ac.uk

Please refer to the following web pages for information regarding the Principal investigators and their research interests.

Resource Brief description Maintained by

Databases

ALIGN A compendium of sequence alignments Attwood Group
CADRE Aspergillus genomic data CADRE Team
Chick web site Gallus gallus ESTs Dr Simon Hubbard
Drosophila DNaseI footprint data base Genome annotation of transcription factor binding sites in Drosophila Bergman Group
fuGIMS Multiple fungal species e-fungi Group
miRBase MicroRNA nomenclature, sequences and annotation
 Griffiths-Jones group
OWL Composite protein sequence database Attwood Group
Phosphabase A protein phosphatase information resource
PrePRINTS An automatically generated supplement to the PRINTS database Attwood Group
PRINTS Protein motif fingerprint database Attwood Group
PRINTS-S PRINTS relational cousin Attwood Group

Database search tools

FingerPRINTScan PRINTS fingerprint search tool Attwood Group
PRINTS BLAST BLAST search tool for PRINTS Attwood Group
Pepmapper A protein search tool which uses Mass Spec. data produced by the digestion of a protein to identify a match to a protein from a database. Julian Selley

Sequence analysis and visualisation software

CINEMA5

Colour INteractive Editor for Multiple Alignments Attwood Group
CTree Visualization and cluster analysis of phylogenetic tree topology John Archer
JNets A tool for visualising, manipulating and analyzing networks by overlaying annotation Jamie MacPherson
Leaphy A program for inferring phylogenetic trees from molecular sequence data Simon Whelan
Pepseeker A tool for finding matching peptides and/or proteins matching various entered alternative properties Julian Selley
PHASE Bayesian and maximum likelihood phylogenetic inference package Rattray Group
RALEE RNA ALignment Editing in Emacs Griffiths-Jones group
Siteseer Visualisation and analysis of transcription factor binding sites in nucleotide sequences Craig Lawless
Recombination programs Links to recombinant sequence analysis/detection programs Robertson Group
UTOPIA A collection of interactive tools for analysing protein sequence and structure Advanced Interfaces Group

Microarray analysis

AffyDEComp Benchmark for comparing differential expression methods on Affymetrix data Richard Pearson
MADAT Microarray Data Analysis Tool for affymetrix data analysis Brass Group
MaxD A data warehouse and visualisation environment for microarray expression data Brass Group
PUMA Propagating Uncertainty in Microarray Analysis Rattray Group

Network visualisation

Interview An interactive tool for producing 2D layouts of network data. John Pinney
OptiMage A tool for producing 3D layouts of network data. John Pinney
TVi Visualisation of network data in a phylogenetic context. John Pinney

Structural biology

Elephant EmpiricaL Enhancement of Predicted HelicAl N-Termini Vicki Mckenna
Crescendo A program for identifying functional sites in proteins Lovell Group
Cupins Superfamily Comparative modelling study Warwicker Group
intcalc Prediction of protein-protein binding energy for a specified interface Warwicker Group
naccess Calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. Simon Hubbard
Nickpred A tool in the understanding of limited proteolysis Simon Hubbard
PhosPatch A tool to analyse the charge and accessibility around potential phosphorylation sites Warwicker Group
Segno A geometry-based method for assigning secondary structure in Proteins Lovell Group

Workflow management

myGrid A knowledge rich, Grid enabled platform Goble Group

Text mining and annotation tools

BioIE Extracting sentences from the biomedical literature Attwood Group
METIS Multiple Extraction Techniques for Informative Sentences Attwood Group
PRECIS An automated annotation system which generates protein reports from sets of related SWISS-PROT entries Attwood Group

Bioinformatics tutorials

EMBER European Multimedia Bioinformatics Education Resource EMBER Consortium
A taste of Bioinformatics Interactive Bioinformatics tutorial Attwood Group