Align and visualize multiple (mitochondria) nucleotide sequence (.fasta) files #7
Description
Background
Looking at genetic alignments is a very important part of molecular biology. The human eye can pick up patterns on a small scale, then we can program the computer to pick out similar patterns on a much larger scale.
Making alignments creates an indexed location for each nucleotide in a fasta file. In turn, this will allow downstream processing like determining the distance between two sequences.
Aim
Align the 9 .fasta files in this folder:
mitolin/data/gen/nguyen_nc_2018/20190702-fastas-on-hpc/1739/20lines/
Related to issue 5
Related to issue 1 fluHA
Method
You can start with Blast or Muscle. Muscle will generate a sequence distance score that can be used to make a lineage tree (aka dendogram/hierarchical clusters).
Wikipedia has a list of alignment visualization software here.
Document your work
Please fork & clone this repo. Check out a branch for your work, then push and make a PR for us to merge your note and files.
Add a note (can be .md or .ipynb) with your solution to mitolin/nb.
Your note should be named as follows:
- DATE-issue#-shortdescription.ext
e.g.:
- 20190701-i02-extract-chrM-fa.md
Questions?
Please put questions related to this issue in this issue thread. If you want a quick response, post a link to your comment in this thread to Slack #deepcelllineage or DM @deena. To join Slack enter your email address here. For questions NOT specifically related to this issue, get in touch through any of the communication methods listed in DCL's overview README.