SMART is a program used to compute supermaximal k-mismatch repeats given a DNA or Protein sequence.
Installation: To compile SMART, please follow the instructions given in file INSTALL.
INPUT: A sequence in FASTA format. The input file is specified using the -i option.
OUTPUT: A BED file containing statistics of supermaximal repeats computed. The output file is specified using the -o option.
Columns 1 and 3: Length of supermaximal repeat.
Column 2: Starting position of the first supermaximal repeat.
Column 4: Starting position of the second supermaximal repeat.
Column 5: Number of mismatches between the pair of supermaximal repeats.
Column 6: Identity score of the pair of supermaximal repeats.
Column 7: Raw score of the pair of supermaximal repeats.
Column 8: E-value of the pair of supermaximal repeats.
Usage: smart <options>
Available options:
-i <file> fasta/fastq input file
-o <file> output file
-l <int> minimum length of supermaximal repeats
-k <int> maximum number of mismatches
-r <int> 0 for O(n) space for rmqs. 1 for O(nlogn) space for rmqs. Default: 1
-t <int> 0 not to trim to optimize e-value and 1 to trim to optimize e-value. Default: 1
-h help
Example:
./smart -i ./data/ecoli.fasta -o ecoli.out -k 1 -l 1000
Citation
Lorraine A K Ayad, Panagiotis Charalampopoulos, Solon P Pissis
SMART: SuperMaximal Approximate Repeats Tool
Bioinformatics, Volume 36, Issue 8, 2020
https://doi.org/10.1093/bioinformatics/btz953
License: GNU GPLv3 License; Copyright (C) 2019 Lorraine A.K. Ayad, Panagiotis Charalampopoulos and Solon P. Pissis.