GEANFAMMER

GEANFAMMER stands for GEnome ANalysis and Protein FAMily MakER. It has been developed for the analysis of most of the complete bacterial genomes announced since 1995. It summarises the whole procedure of preparing statistically and biologically more relevant protein (sequence) duplication modules before any more biological analysis like structure and function assignment. With this now anybody can easily analyse the duplication level and types of sequence families in any genome or database.
This is critically important as a lot of protein sequences are multidomain and it can cause serious problems in analysing large amount of sequences automatically if sequences were not broken down to sequence domains.

Availability

Geanfammer is written in perl5 and is available from the CPAN perl archive or via the author´s web site. The program and its modules/subroutines are free for academic research and educational institutes for non-profit making purposes.

 Information by: Jong H. Park

Resources and further information

• Harvard Medical School
  http://www.med.harvard.edu/
• Geanfammer homepage
  http://cyrah.med.harvard.edu/Proj/Bio/Geanfammer/
• Download Geanfammer from MRC-LMB (UK)
  ftp://ftp.mrc-lmb.cam.ac.uk/pub/genomes/Software/Gea nfammer/
• Download Geanfammer at CPAN
  ftp://unix.hensa.ac.uk/mirrors/perl-CPAN/authors/Jong_ Park/
• Reference:
• Park, J. and Teichmann, S.A. DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- or multi-domain proteins. Bioinformatics, 14, 144-150

Direct questions or comments to Bioinformer Editor. This page last modified Friday, 16 July, 1999.
ISSN 1462-1363. More information about the BioInformer.

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