motiflocation

A small program to find motif locations in FASTA files.

Usage

To compile, you should just be able to type 'make'.

Usage is as follows:

./motiflocation -file1 <fasta_file> -startstr <motif> -out <out_file>

• Parameters

  • -file1 : Specify the input fasta file.
  • -startstr : Specific the motif to find in the fasta file.
  • -out : Specify the output file

• Optional parameters

  • -chr : Specify the chromosome on which to run the algorithm.
  • -mutations : Specify the number of mutations (mismatches) to allow when finding motifs.
  • -uppercase_only : Only report uppercase matches.
  • -lowercase_only : Only report lowercase matches.

Output

The program produces an output file with 5 columns.

1. Chromosome
2. Motif start position
3. Motif end position
4. Strand
5. Motif sequence