Resources
The following list contains links to the on-line resources provided by our research group.
Please refer to the following web pages for information regarding the Principal investigators and their research interests.
Should any of the links be broken or for general enquiries please contact bioinformatics-webmaster@manchester.ac.uk.
- Databases
- Database search tools
- Sequence analysis and visualisation software
- Microarray analysis
- Network visualisation
- Structural biology
- Work management
- Text-mining and annotation tools
- Bioinformatics tutorials
| 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 |
| 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
| 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 |
| 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 |