README.INSTALL

(Full documentation with examples is in the doc/ directory)

ISseeker

ISseeker is designed to find partial Insertion Sequences (IS) in contigs, then use the flanking 
sequences around them to determine where they were inserted against one or more reference sequences (e.g. 
a chromosome reference along with some plasmids).

It blasts the Insertion Sequence (IS) against a collection of genome contigs in a multi-FASTA file, then 
extracts the flanks and blasts them against the references. Pairs of flanks that are oriented correctly and 
are within 10 bases will be joined as begin-end flank pairs that indicate an insertion event.



ISseeker requires these PERL modules to run (all available from CPAN):


Bio::SeqIO
Config::General
Cwd
File::Basename
Getopt::Long
List::Util
Log::Log4perl
Text::CSV
Class::Accessor


If you do not wish to (or cannot) install these in your PERL system libraries, you can install them in the ISseeker perllib/ directory and they will be used from there,



ISseeker requires the following applications to run:

extractseq (from the EMBOSS package: http://emboss.sourceforge.net/)
blastall & formatdb (from NCBI’s blast package: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/)

The locations of these executables must be set in the config file bin/ISseeker.cfg for the application to run.