- NAME
- SYNOPSIS
- DESCRIPTION
- EXAMPLES
- OPTIONS
- EXIT STATUS
- AUTHORS
- REFERENCES
- VERSION INFORMATION
- SEE ALSO
- LICENSE
NAME
nasp - NASP (Nucleic Acid Structures Predictor)
SYNOPSIS
nasp [OPTIONS] FILE
DESCRIPTION
NASP takes as input a nucleotide sequence alignment and determines:
(1) The over-all probability that the sequences within the alignment possess a degree of secondary structure that cannot be accounted for by chance;
(2) the list of most probable evolutionarily conserved secondary structures within the sequences.
EXAMPLES
Compute only consensus structures:
nasp alignment.fas
Compute consensus structures and p-values:
nasp -P -it 100 -th 0.05 alignment.fas
Using multiple processors (e.g. 4) in an MPI environment (e.g. OpenMPI):
mpirun -np 4 nasp -P alignment.fas
OPTIONS
Usage: nasp [OPTIONS] <file>
-h, --help Print complete help and exit. --version Print version info and exit. -mpi, --mpi Flag to force the use of parallel computation. This assumes that MPI libraries are installed. While NASP tries to find out whether it is running in an MPI environment or in serial mode, it might not identify some MPI implementations. This flag enables the user to enforce the use of MPI in such cases. It is recommended to use it whenever running NASP in an MPI environment. -n, --seqtype Sequence type: RNA | DNA (case insensitive). The nucleic acid sequence type. Tells the program whether sequences should be considered as either RNA or DNA, the default is set to RNA. The valid nucleotides are A, C, G, T and U (case are irrelevant), any other symbol will be ignored. This option is used in the call to hybrid-ss or hybrid-ss-min from UNAfold. Default is: <RNA> -t, --temperature Folding temperature -- in degree Celsius -- in range [0,100]. This option is used in the call to hybrid-ss or hybrid-ss-min from UNAfold. Default is: <37> -C, --circular Flag that specifies that the sequence is circular, as opposed to linear (default). This option is used in the call to hybrid-ss or hybrid-ss-min from UNAfold. -N, --Na Sodium ion concentration (in mol/L) in range [0,20] (e.g. the concentration of sodium in human blood plasma is ~ 0.3 mol/L). This option is used in the call to hybrid-ss or hybrid-ss-min from UNAfold. Default is: <1> -M, --Mg Magnesium ion concentration (in mol/L) in range [0,20] (e.g. the concentration of magnesium in human cells is ~ 0.004 mol/L). This option is used in the call to hybrid-ss or hybrid-ss-min from UNAfold. Default is: <0> -P0, --P0 Base-pairing probability threshold in range (0,1]. It is the probability value above which a base-pairs is accepted. This value is only used for sequences smaller than 4000 Default is: <0.0001> -P, --pvalue Flag that enables the computation of p-values by randomly shuffling the alignment. The p-values indicate the probability that no additional unaccounted for structures remain within the analysed sequencesNote that this significantly increases nasp's running time. The shuffling strategy may be defined by the option --shuffle (-sh). -th, --threshold P-value threshold in range [0,1]. It determines the probability level at which ends the iterative enrichment for evolutionarily conserved secondary structures. This option is only used when the flag --pvalue (-P) is also specified. Default is: <0.05> -it, --iterations Number of permutations to perform to compute the p-values. This option is only used when the flag --pvalue (-P) is also specified. Default is: <100> -sh, --shuffle Indicates the alignment column shuffling strategy to be carried out. Possible strategies are: 1=mono-nucleotide shuffling | 2=di-nucleotide shuffling. This option is only used when the flag --pvalue (-P) is also specified. Default is: <1> -split, --split-length Minimum length of the sub-sequences used when computing the p-values. Special values are: -1=do not split | 0=automatic. If --split-length >= 0, then the MFE computation for shuffled sequences is performed indirectly by splitting them into sub-sequences. The splits are chosen such that existing structures are not disrupted. The MFEs of the sub-sequences are computed separately and summed-up to give the MFE of the complete sequence. Default is: <0> -s, --max-structure Maximum number of structures to consider. Default is: <1000> -min, --min-length The minimum length allowed for a sub-structure (e.g. if set to an integer greater than 1, it means avoiding isolated base-pairs). Default is: <2> -lo, --min-loop Minimum length of a loop for a struture to be considered. Default is: <3> -d, --dvalue Adjustment depth 'd' to apply to the consensus matrix. All nucleotides falling within 'd' bases up-stream or down-stream of a given nucleotide are considered to be its potential homologues. Default is: <0> -mat, --matrix-only Flag to only compute the consensus matrix. -v, --verbose Verbosity level. Use value 99 for maximum output (debugging). Default is: <1> --restore Flag to restore previous workspace. Useful to recover from errors and debug (EXPERIMENTAL)
EXIT STATUS
nasp returns a zero exist status if it succeeds. Non zero is returned in case of failure.
AUTHORS
Jean-Yves Semegni (initial version), Renaud Gaujoux (refactored and optimized version)
REFERENCES
1. J. Y. Semegni; M. Wamalwa; R. Gaujoux; G. W. Harkins; A. Gray; D. P. Martin (2011). NASP: A parallel program for identifying evolutionarily conserved nucleic acid secondary structures from sequence alignments. Bioinformatics; 2011 27(17): 2443-2445. doi:10.1093/bioinformatics/btr417 http://bioinformatics.oxfordjournals.org/content/27/17/2443.
NASP intensively uses UNAFold, please also cite the following reference when using NASP:
2. Markham,N.R. and Zuker,M. (2008). UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol., 453:3-31.
VERSION INFORMATION
This manpage describes nasp 1.5
SEE ALSO
mpirun(1)
, hybrid-ss(1), hybrid-ss-min(1)
LICENSE
Copyright (C) 2011 Yves Semegni, Renaud Gaujoux
NASP is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
NASP is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with NASP. If not, see <http://www.gnu.org/licenses/>