a generic tool for sequence alignment

A guide to using exonerate in Client-Server mode


Normally when exonerate is run, the query and target sequences are used as fasta files. The run time of any search at least be proportianal to the size of these input files. However, the exonerate-server allows a set of sequences and an index of words which they contain to be held in memory. The server may be used in place of the target database on the exonerate command line, which allows very fast searches to be conducted (with run time independent of the size of the database). To run the exonerate with exonerate-server, you need to build a database file and an index file, and start the server using these files. These steps are explained below:
  1. Building the database (.esd) file
  2. Building the index (.esi) file
  3. Starting the server
  4. Running the client
  5. Running under LSF

Building the database (.esd) file

Building the index (.esi) file

Starting the server

Running the client

Running exonerate-server under LSF

Please email me if you have any questions

Guy St.C. Slater.