/SSWfindsim

Use ssw method find similarity

Primary LanguageC

Find similar segments using SIMD/OpenMP Striped Smith-Waterman algorithm

This project is based on https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library.

Arugments

--center   FILE      center file name (Required)
--seq      FILE      sequence file name (Required)
--out      FILE      output file name (Required)
--matrix   FILE      matrix file name
--thread   N         threads in this program (default 1)
--dna                this file is DNA sequence file
--protein            this file is protein seqeuence file
--help               print help message
--version            show program version

Input and output

  • Input: two files, center (target) file is the base sequence, must have only 1 sequence; sequence (query) file has many ($x$) sequences.
  • Output: one file with $x$ lines, every line contains:
    • sequence_id, which means the number of sequence;
    • query_begin, query_end, which means the place of center sequence;
    • target_begin, target_end, which means the place of query sequence;
    • score, SW score;
  • The order of line is: sequence_id query_begin query_end target_begin target_end score alignment_list.
    • Sample: find the similarity of target sequence AAAATC and query sequence AAAAATC with treated them as DNA sequences:
    • Will print 0 1 6 0 5 12 6M.