Genome Management Package

This tool is copyright 2016 by Nattawet Sriwichai, King Mongkut's University Technology Thonburi (Bioinformatics and Systems Biology Program), Thailand. All rights reserved. See the licence text below.

Usage: Promoter of genes retrieving

Then run python script by used command line on windows or unix::

python3 promoter_retrieve.py \
	--output <output_file.fa> \
	--output_format <fasta/gff> \
	--genome <genome.fa> \
	--gff <genome.gff> \
	--type <TLS/TSS> \
	--upstream <bp> \
	--downstream <bp> \
	--all_gene <Y/N> \
	--selected_gene_list <gene_list.txt, is optional if all_gene is N> \
	--remove_n_gap <Y/N> \
	--min_length <default is 100 bp>

Usage: Get protein or gene sequences from genome

python3 proteins_retrieve.py \
	--input <input_fasta_file> \
	--list_of_interest <list_of_protein_id.txt> \
	--output <output_file.fa>

Usage: Get genome statistic

python3 get_genome_statistic.py \
	--genome <genome.fa>

Licence (MIT)

Copyright (c) 2016 King Mongkut's University technology Thonburi

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.