Authors: Jimmy Ka Ho Chiu, Yi-Ping Phoebe Chen
Chiu, J.K.H. and Y.P.P. Chen, Pairwise RNA Secondary Structure Alignment with Conserved Stem Pattern. Bioinformatics, 2015. doi:10.1093/bioinformatics/btv471
PSMAlign is an open source tool that performs pairwise RNA secondary structures alignment based on the conserved stem pattern discovered. It enables alignment of large structures, such as those in the 23S ribosomal RNA family. Arbitrary pseudoknots are also allowed.
Dot-parentheses (.dp file) format is currently supported.
The command to perform RNA secondary structure alignment is:
perl align.pl <sequence DP file 1> <sequence DP file 2> [-o <output file>] [-t <selection threshold>] [-k <top K value>] [-d|-p]
- selection threshold: a positive integer specifying the minimum size of the initial ECGM obtained in phase 2 of progressive stem matching. Default value is 5.
- K: a positive integer specifying the top-K selection in phase 3 of progressive stem matching. Default value is 1.
- mode: By default progressive stem matching is applied to find the true conserved stem pattern (or the one close to it). If it cannot be found, then the best conserved stem pattern is discovered instead. User can specify only one pattern to be used.
PSMAlign can be downloaded here:
psmalign.tar.gz (for Linux and Mac OS X)
Decompress the downloaded file. No installation is required.
Sample input structure files:
Ribonuclease P RNAs ASE_00194 and ASE_00204 from RNA STRAND database
M. Andronescu, V. Bereg, H. H. Hoos, and A. Condon. RNA STRAND: The RNA Secondary Structure And Statistical Analysis Database. BMC Bioinformatics. 2008;9(1):340.
Jiang T, Lin G, Ma B, Zhang K (2002) A general edit distance between RNA structures. Journal of Computational Biology 9: 371-388.
Copyright © 2014 Jimmy Ka Ho Chiu and Yi-Ping Phoebe Chen