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Attention:
Due to technical maintenance some tools might be unavailable. See maintenance information. 
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GUUGle - Manual
GUUGle efficiently
locates potential helical regions under RNA base pairing rules,
which include Watson-Crick as well as G-U pairs. It takes two
Fasta files as input.
NAME
| GUUGle - finds 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.
If you need to create larger output than we permit for online use, or want to incorporate GUUGle into your own pipeline, please download the GUUGle program from the BiBiServ download department.
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