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The  GEANFAMMER  Package
 

GEnome ANalysis and Protein FAMily MakER

 


If any of these programs are used, please cite "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)".


News on geanfammer development. (July 1998)

. " GEANFAMMER " refers either to a perl5 program*, a suite of perl5 programs, a perl5 module or a perl5 subroutine library. These are all available by anonymous ftp at cyrah.ebi.ac.uk . 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.

Geanfammer uses FASTA or SSEARCH which allow the gap in sequence comparison in compared to older BLASTP algorithm which does not. Also, it uses E value instead of Z-score to increase the sensitivity.
 
  DownloadGEANFAMMER single program . A summary of the single program geanfammer.pl is as follows.

The suite of perl5 programs essentially consists of the constituent parts of the GEANFAMMER single program. A flow chart of the constituent programs can be found by clicking here .


. You can also download geanfammer from CPAN site. However, it might not be as updated as above ftp routes.
 
 
 

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Bug report -->  sat@mrc-lmb.cam.ac.uk , jong@mrc-lmb.cam.ac.uk



 
 

Sarah A. Teichmann & Jong H. Park
1st/Oct/1997.

(C) Copyright. 1995.