BP_FLANKS(1p)						User Contributed Perl Documentation					     BP_FLANKS(1p)

NAME

       flanks - finding flanking sequences for a variant in a sequence position

SYNOPSIS

	 flanks --position POS [-p POS ...]  [--flanklen INT]
		accession | filename

DESCRIPTION

       This script allows you to extract a subsequence around a region of interest from an existing sequence. The output if fasta formatted
       sequence entry where the header line contains additional information about the location.

OPTIONS

       The script takes one unnamed argument which be either a file name in the local file system or a nucleotide sequence accession number.

	 -p	    Position uses simple nucleotide sequence feature table
	 --position notation to define the region of interest, typically a
		    SNP or microsatellite repeat around which the flanks are
		    defined.

		    There can be more than one position option or you can
		    give a comma separated list to one position option.

		    The format of a position is:

			[id:] int | range | in-between [-]

		    The optional id is the name you want to call the new
		    sequence. If it not given in joins running number to the
		    entry name with an underscore.

		    The position is either a point (e.g. 234), a range (e.g
		    250..300) or insertion point between nucleotides
		    (e.g. 234^235)

		    If the position is not completely within the source
		    sequence the output sequence will be truncated and it
		    will print a warning.

		    The optional hyphen [-] at the end of the position
		    indicates that that you want the retrieved sequence to be
		    in the opposite strand.

	 -f	    Defaults to 100. This is the length of the nucleotides
	 --flanklen sequence retrieved on both sides of the given position.

		    If the source file does not contain

OUTPUT FORMAT

       The output is a fasta formatted entry where the description file contains tag=value pairs for information about where in the original
       sequence the subsequence was taken.

       The ID of the fasta entry is the name given at the command line joined by hyphen to the filename or accesion of the source sequence. If no
       id is given a series of consequtive integers is used.

       The tag=value pairs are:

       oripos=int
	  position in the source file

       strand=1|-1
	  strand of the sequence compared to the source sequence

       allelepos=int
	  position of the region of interest in the current entry.  The tag is the same as used by dbSNP@NCBI

       The sequence highlights the allele variant position by showing it in upper case and rest of the sequence in lower case characters.

EXAMPLE

	 % flanks ~/seq/ar.embl

	 >1_/HOME/HEIKKI/SEQ/AR.EMBL oripos=100 strand=1 allelepos=100
	 taataactcagttcttatttgcacctacttcagtggacactgaatttggaaggtggagga
	 ttttgtttttttcttttaagatctgggcatcttttgaatCtacccttcaagtattaagag
	 acagactgtgagcctagcagggcagatcttgtccaccgtgtgtcttcttctgcacgagac
	 tttgaggctgtcagagcgct

TODO

       The input files are assumed to be in EMBL format and the sequences are retrieved only from the EMB database. Make this more generic and use
       the registry.

       head1 FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing lists  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho
       Email:  <heikki-at-bioperl-dot-org>

perl v5.14.2							    2012-03-02							     BP_FLANKS(1p)