

GUUGle takes two Fasta files as input.


NAME
	 GUUGle - find all exact matches (under RNA base pairing rules) of a minimal length between two sets of RNA sequences

SYNOPSIS
     guugle [OPTION]... TARGET QUERY

DESCRIPTION
     TARGET and QUERY are Fasta files containing RNA sequences
	 (Nucleotided T will be converted to U internally and will shown as U in the output.)
	 
     -d x, obligatory, output matches with length of at least x

	 -e y, switch output mode, show target seeds extended by y bases in either direction
	 
	 -l z, limit output to first z matches
	 
	 -s, show match length distribution
	 
	 



The option "-d x" is obligatory. x is the minimal length of matches between target and query sequences. The output looks like this:

options: "-d 7"
---------------------------
MatchLength: 7 "ENST00000309834.1|EN" at 57 vs. "hsa-let-7a_seed" at 1 
5cugucuc3
3gauggag5

MatchLength: 7 "ENST00000309834.1|EN" at 40 vs. "hsa-let-7a_seed" at 1 
5uuaccuu3
3gauggag5
---------------------------



If option "-e y" is used, the output mode changes. The matching target sequences are reported, and extended by y bases in either direction, if possible. The output now is in Fasta format:

options: "-d 4 -e 3"
---------------------------
> ENST00000330364.1|EN_at_120
cacaccuuuua

> ENST00000330364.1|EN_at_29
uaaacuucccc

> ENST00000309834.1|EN_at_36
uucacuuuuac

> ENST00000309834.1|EN_at_24
cgcaucugaa

> ENST00000309834.1|EN_at_55
ucaaucuguc
---------------------------
(4 bases(matching seed) + 2 * 3 bases(extension) = 10 bases !)


"-l" limits the number of matches that will be reported.


"-s" shows the match length distribution.
