Introduction
PLEXY is a tool for computation of optimal thermodynamical interactions of a box C/D snoRNA with a putative target RNA.
It is based on RNAPLEX.
Download
download PLEXY (new -T option included)
Be sure to have the latest version of RNAPLEX installed.
Executables of RNAPLEX should either be installed in the same directory or you have to provide the correct $PATH at the beginning plexy.pl.
Input sequences
To perform a target prediction you have to provide:
- one or more putative target sequence(s) in fasta format and
- one or more snoRNA sequences also fasta formatted.
The header of each snoRNA sequence has to
contain D-
and/or Dprime-
box annotation(s). The box annotation must be seperated with
_ and have to be located at the end of the header line. The first
two parts are taken for snoRNA_id, everything else does not matter at all.
Example:
>U95_H.sapiens_(chr5)_180602916,180602983_-_GTGCTGA_36_CTGA_26_GTGATGA_5_CTGA_59
GGCGGTGATGACCCCAACATGCCATCTGAGTGTCGGTGCTGAAATCCAGAGGCTGTTTCTGAGCTGCC
Usage
plexy.pl -o [directory/] -f [fa-file] -t|T [directory/|fa-file]
- -f : input fasta-file with CD-box snoRNA sequences
- -o : directory for output files
- -t : directory with putative target RNA sequences in fasta format (or use -T)
- -T : single file with putative target RNA sequences (or use -t)
OPTIONAL
- [-l] : option for large datasets. Results are not kept in the
memory during runtime but are returned directly and the output is
reduced. This makes it possible to search transcript wide, but the
results need some postprocessing as interactions are not unique and not
sorted for mfe values.
- [-p] : directory containing accessibility-profiles (RNAplfold)
- [-e] : MFE-treshold, only targets with better MFE are shown, default value is -7.70
Output
without -l option: (sorted, unique and nice)
./plexy.pl -f U95.fa -o temp/ -T allTargets_human.fa -e -20.00
#D-box targets:
U95-1_H.sapiens D H_sapiens_28S-2802 -23.40 (((((((((((((.&.))))))))))))) GAACAmGCCTCTGGC&TCCAGAGGCTGTTT
#D'-box targets:
U95-1_H.sapiens D' H_sapiens_28S-2811 -20.10 .(((((((((((.&.))))))))))). CTGGCmATGTTGGA&CCCAACATGCCAT
#D-box targets:
U95-2_H.sapiens D H_sapiens_28S-2802 -23.60 (((((((((((((.&.))))))))))))) GAACAmGCCTCTGGC&CCCAGAGGCTGTTT
#D'-box targets:
No targets found!
with -l option: (not sorted, not unique and not so nice, but machine readable and gentler to your memory, especially during runtime)
./plexy.pl -f U95.fa -o temp/ -t /path/human_targetRNAs/ -e -20.00 -l
#D-box targets:
U95-1_H.sapiens|D|H_sapiens_28S-2802|-23.40|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&TCCAGAGGCTGTTT
U95-1_H.sapiens|D|H_sapiens_28S-2802|-23.40|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&TCCAGAGGCTGTTT
U95-1_H.sapiens|D|H_sapiens_28S-2802|-22.30|((((((((((((.&.))))))))))))|AACAmGCCTCTGGC&TCCAGAGGCTGTT
U95-1_H.sapiens|D|H_sapiens_28S-2802|-23.40|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&TCCAGAGGCTGTTT
U95-1_H.sapiens|D|H_sapiens_28S-2802|-23.40|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&TCCAGAGGCTGTTT
U95-1_H.sapiens|D|H_sapiens_28S-2802|-23.40|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&TCCAGAGGCTGTTT
U95-1_H.sapiens|D|H_sapiens_28S-2802|-23.40|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&TCCAGAGGCTGTTT
U95-1_H.sapiens|D|H_sapiens_28S-2802|-22.90|(((((((((((((&)))))))))))))|GAACAmGCCTCTGG&CCAGAGGCTGTTT
#D'-box targets:
U95-1_H.sapiens|D'|H_sapiens_28S-2811|-20.10|.(((((((((((.&.))))))))))).|CTGGCmATGTTGGA&CCCAACATGCCAT
#D-box targets:
U95-2_H.sapiens|D|H_sapiens_28S-2802|-23.60|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&CCCAGAGGCTGTTT
U95-2_H.sapiens|D|H_sapiens_28S-2802|-23.60|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&CCCAGAGGCTGTTT
U95-2_H.sapiens|D|H_sapiens_28S-2802|-23.60|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&CCCAGAGGCTGTTT
U95-2_H.sapiens|D|H_sapiens_28S-2802|-23.60|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&CCCAGAGGCTGTTT
U95-2_H.sapiens|D|H_sapiens_28S-2802|-23.60|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&CCCAGAGGCTGTTT
U95-2_H.sapiens|D|H_sapiens_28S-2802|-23.60|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&CCCAGAGGCTGTTT
U95-2_H.sapiens|D|H_sapiens_28S-2802|-23.60|(((((((((((((.&.)))))))))))))|GAACAmGCCTCTGGC&CCCAGAGGCTGTTT
U95-2_H.sapiens|D|H_sapiens_28S-2802|-22.90|(((((((((((((&)))))))))))))|GAACAmGCCTCTGG&CCAGAGGCTGTTT
#D'-box targets:
No targets found!
Contact
If you have any kind of problems or suggestions how to improve PLEXY feel free to send a mail to steffi@bioinf.uni-leipzig.de