Bioinformatics analysis tools

An account with the Computational Biology Research Group, allows you to log on to our server to use the bioinformatics tools that we provide.

We provide a wide variety of tools, some of which are web-based and some which may be accessed via Unix.

Web analysis tools:

Unless stated, you will need your molbiol username and password to use these tools:

BioArray Software Environment - Microarray analysis   - BASE (NB: specific BASE account required to log on)   - BASE users guide   |   BASE Tutorial (pdf )

Basic Sequence Alignment Search Tool.   - Run BLAST - search the sequence databases held by CBRG   - BLAST introduction - program descriptions and options   - BLAST-searchable databases

European Molecular Biology Open Software Suite.   - EMBOSS Explorer - bioinformatics tools   - Compare EMBOSS and GCG tools   - Bioinformatics FAQ - which EMBOSS tool to use?

GBrowse - Genome browser   - GBrowse databases

Mascot - mass spectrometry searches   - Peptide mass fingerprint search   |   MS/MS ion search   - CPF - Central Proteomics Facility

The following applications have been delevoped by CBRG staff in collaboration with members of the Medical Sciences Division.   - ANALOG - bioinformatics analysis history for individual molbiol users   - WMD - Weapon of Mutant Detection

External:

Sequence Retrieval System at the European Bioinformatics Institute.   - SRS at EBI - search for sequences

UNIX applications:

A wide range of bioinformatics analysis software is available via an account with CBRG. If you are unfamiliar with your CBRG Unix account, please see the guides to logging on to molbiol for PC users and mac users.

• To read brief information about a particular package as well as notes (if any) on its local installation, type about followed by the name of the bioinformatics package, e.g. about readseq. Typing about alone will list all packages on the server (with a couple of exceptions).
  


• To read help on a particular program, in many cases, type the program name with option --help or -help. For example, blastall --help will display the arguments that may be used with blastall.
  


• A CBRG convention is that all programs in a bioinformatics package are installed in /package/Programname/Version/bin. For example, all BLAST 2.2.9 programs may be found in "/package/blast/2.2.9/bin". To run a program, simply type the program name with its required options or arguments. A full list of the available programs can be found here
  


• If a package has more than one version installed, the system sets up a default version. If, for some reason, you want to use a non-default version, then the command usepkg may be used. To use EMBOSS 2.8.0 rather than (the default) 2.9.0, type usepkg emboss 2.8.0. Typing usepkg alone will show you how to use this command.