MolecularMethodsInGenomeResearch

This directory contains teaching materials for a practical course about lab methods in genome research. Besides a set of slides for presentation in class, there are scripts which are needed to perform basic bioinformatic analysis. The concept behind this course and additonal details about the content are included in a publication: https://doi.org/10.1515/jib-2019-0005

Feel free to use any of the provided materials in your own courses.

Extraction of sequences for primer design

This script allows the extraction of a region of interest for primer design and other applications.

Usage
python3 seqex3.py --in <FILE> --out <FILE> --contig <STR> --start <INT> --end <INT>

Mandatory:
--in       STR   Input FASTA file.
--out      STR   Output FASTA file.
--contig   STR   Sequence ID
--start    INT   Start position
--end      INT   End position

--in specifies the input FASTA file for the sequence extraction. Sequence IDs will be split at the first space.

--out specifies the output FASTA file. Extracted sequence parts will be stored in this file.

--contig specifies the sequence ID of a target sequence. A part of this sequence will be extracted. The sequence ID will be splitted at space, tab, or colon.

--start specifies the start position of the region of interest. This value must be smaller than the --end value.

--end specifies the end position of the region of interest. This value must be larger than the --start value.

References:

https://doi.org/10.1371/journal.pone.0164321

https://www.biorxiv.org/content/early/2018/09/06/407627

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0030196