Introduction
LoopOut is simple comand line program to allow potential FISH probes to be screened for non-target binding at off target sites containing single nucleotide insertions or deletions. Site containing insertions and deletions are not detected by the major FISH probe design software eg ARB (Ludwig et al., 2004) and probeCheck (Loy et al., 2008). FISH probes can bind efficently to such sites if the free energy of the loop structure is less than 4 kcal/mol leading to false postives. LoopOut is described in Non-target sites with single nucleotide insertions or deletions are frequently found in 16S rRNA sequences and can lead to false positives in fluorescence in situ hybridization (FISH), McIlroy et al. 2010.
Update December 2011. LoopOut has been updated to 0.52. Basically nothing major, just a few bug fixes.
UsE
>loopout [options] -s [probe sequence]
Windows
To run LoopOut under Windows you will need to open a cmd shell (type cmd in Run). You will need to change to the directory where the loopout program is located (i.e. cd C:/loopout/). Then type loopout followed by the options and the probe sequence in the cmd shell window.
MacOS X
To run Loopout on MacOS X download the appropriate version for your machine (Intel or PPC). You will then need to open a terminal window and cd to the folder containing the loopout program. Then type loopout followed by the options and the probe sequence in the terminal window.
options
-n [oligo name]
-s [oligo sequence]
-b [inserted base]
-i [insert position]
-d [deletion position]
-o [output file | screen]
-h [help]
Downloads
Apple Mac OS X - Intel
Apple Mac OS X - PPC
Windows 2000, XP, Vista, Windows 7
x86 Linux
last updated December 6, 2011 | Copyright © 2011 ribosome.org