WebBSS requires a truncated version of FPC file. The ScriptDir/trunc_fpc.pl reads the FPC file and outputs a file 'BSS.fpc' with only the necessary information. This file is in <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/Data directory.

WebBSS runs BSS searches via FPC's batch mode function. For more details on BSS refer to the BSS tutorial.

FILE FORMATS & CONFIG   Back to top

The following config variables are used: FPC_FILE, BES_FILE_PATH, GENOME_FILE_PATH, WEBBSS_SEQ_FILE.

All files in this section are put into the <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME> directory by the setup.pl script, and can later be changed by the user (Note: the update.sh needs to be rerun after a change). This directory will be referred to as the MAP directory in the following discussion.

BES Files:

You specify a directory of BES files in the BES_FILE_PATH variable of the configuration file. The BES files should be in FASTA format and files should have ".bes" extension.
To associate a BES with a clone name, the clone name in FPC must a substring of the BES name. For example, clone a0001a01 in FPC has the BES OSJNBa0001a01.f and OSJNBa0001a01.r. The setup.pl will make a soft link to the directory in <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/Data directory.

Sequence Files:

The sequence clones must be in FPC as simulated digest (SD) clones. This can be done for agarose gels using the FSD program. (For HICF, contact us). The clone is entered into FPC with its GenBank name followed by "sd".

You specify a directory of sequence files in the GENOME_FILE_PATH of the configuration file. The sequence files must be named by their GenBank accession number, though they can have a suffix, e.g. AC00000.seq. The BSS will match this to the FPC clone AC0000sd1. The setup.pl will make a soft link to the directory in <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/Data directory.

Sample Files:

You specify a file name for the example file in the WEBBSS_SEQ_FILE variable of the configuration file. You will want to use a file that you know will have a hit to either one or more BESs. This is the file that is used when the "Load Example Sequence" is selected on the WebBSS page.