- Python 3.5+
- MacOS or Linux OS
- EMBOSS: http://emboss.sourceforge.net/download/
- reference (fasta-list) must be converted to single-line mulit-fasta format: https://www.biostars.org/p/9262/
usage: pseudoSearch.py [-h] --query QUERY --fasta_list FASTA_LIST
[--nmer NMER]
Finding the Longest kmer
optional arguments:
-h, --help show this help message and exit
Input/Output:
--query QUERY Gene 1
--fasta_list FASTA_LIST
Gene 2
--nmer NMER Percent Minimum Perfect Match
python pseudoSearch.py --query /Data/Homo_sapiens_NCF1B_sequence.fa --fasta_list /Reference/hg19.fa --nmer 5