A small program to find motif locations in FASTA files.
To compile, you should just be able to type 'make'.
Usage is as follows:
./motiflocation -file1 <fasta_file> -startstr <motif> -out <out_file>
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Parameters
- -file1 : Specify the input fasta file.
- -startstr : Specific the motif to find in the fasta file.
- -out : Specify the output file
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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.
The program produces an output file with 5 columns.
- Chromosome
- Motif start position
- Motif end position
- Strand
- Motif sequence