BLISTR

BLurry Imperfect Short Tandem Repeats in DNA and Protein sequences

Motivation

XXX

Getting Started

Prerequisite

The only dependency for BLISTR is zlib, which is used for handling gz-compressed files.

Installation

git clone https://github.com/Wenfei-Xian/BLISTR.git  
cd BLISTR/src  
make

Installation with Bioconda (on the way)

conda install BLISTR  

Usage

Input Files

DNA or protein sequences in fasta format, which can be compressed in gz format.

Running BLISTR

BLISTR perfect_str_default -f test.fa > test.fa.blistr.out

Identify tandem repeats of amino acid on uniprot set

wget https://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/complete/uniprot_sprot.fasta.gz
BLISTR fuzzy_str_default -f uniprot_sprot.fasta.gz > uniprot_sprot.fasta.blistr.fuzzy.out

Available Commands:

BLISTR: BLurry Imperfect Short Tandem Repeats
Usage: BLISTR <command> [options]
Command:
	perfect_str_default <options>
	perfect_custom <options>
	fuzzy_str_default <options>
	fuzzy_custom <options>

Available Options:

perfect_str_default

BLISTR: BLurry Imperfect Short Tandem Repeats
Usage: BLISTR perfect_str_default <options>
	unit length range is 1-6bp and copy number threshold is 10,5,4,3,2,2
Options:
       -f string     fasta format file (mandatory)
       -s int        whether output the flanking sequence of SSR region (default value: 0 -> don't output; length of flanking sequences -> output)
       -u int        whether replace all letters with uppercase letters (default value: 0 -> don't replace; 1 -> replace)
       -r int        whether output the reverse complement sequence (default value: 0 -> don't output; 1 -> output)

perfect_custom

BLISTR: BLurry Imperfect Short Tandem Repeats
Usage: BLISTR perfect_custom <options>
Options:
       -f string     fasta format file (mandatory)
       -l int        maximum length of SSR unit, example: -l 10 (mandatory)
       -c string     copy threshold for each unit, example: -c 10,5,4,3,2,2,2,2,2,2 (mandatory)
       -s int        whether output the flanking sequence of SSR region (default value: 0 -> don't output; length of flanking sequences -> output)
       -u int        whether replace all letters with uppercase letters (default value: 0 -> don't replace; 1 -> replace)
       -r int        whether output the reverse complement sequence (default value: 0 -> don't output; 1 -> output)

fuzzy_str_default

BLISTR: BLurry Imperfect Short Tandem Repeats
Usage: BLISTR fuzzy_str_default <options>
	unit length range is 1-6bp, copy number threshold is 12,6,4,3,2,2, percentage of imperfect threshold is 0.3,0.4,0.5,0.5,0.5,1, edit distance of each unit is 1,1,1,1,1,1
Options:
	-f string     fasta format file (mandatory)
	-u int        whether to replace all letters with uppercase letters (default value: 0 -> don't replace; 1 -> replace)
	-s int        whether output the flanking sequence of SSR region (default value: 0 -> don't output; length of flanking sequences -> output)
	-r int        whether output the reverse complement sequence (default value: 0 -> don't output; 1 -> output)

fuzzy_custom

BLISTR: BLurry Imperfect Short Tandem Repeats
Usage: BLISTR fuzzy_custom <options>
Options:
	-f string     fasta format file (mandatory)
	-l int        maximum length of SSR unit, example: -l 6 (mandatory)
	-c string     copy threshold for each unit, example: -c 12,6,4,3,2,2 (mandatory)
	-p string     percentage of imperfect units, example: -p 0.3,0.4,0.5,0.5,0.5,1 (mandatory)
	-e string     edit distance for each unit, example: -e 1,1,1,1,1,2 (mandatory)
	-d int        Maximum distance between two seperate STR regions, using negative value for overlapping STRs, example: -d -4
	-u int        whether to replace all letters with uppercase letters (default value: 0 -> don't replace; 1 -> replace)
	-s int        whether output the flanking sequence of SSR region (default value: 0 -> don't output; length of flanking sequences -> output)
	-r int        whether output the reverse complement sequence (default value: 0 -> don't output; 1 -> output)

Contact

Questions, suggestions are welcome by raising an issue on the github page.