InaMBerry
commented
9 years ago Classification: UNCLASSIFIED Caveats: NONE
http://www.ncbi.nlm.nih.gov/nuccore/KJ189367.1
I think output should be in the table format, as Dereje will make it for the tool. So we have a table that shows pos# and its amino acids, and the gene name can be in a column of its own for that position. Thanks! ina
Dr. Irina Maljkovic Berry Lead Scientist, Bioinformatics CNTS Viral Diseases Branch Walter Reed Army Institute of Research Silver Spring, MD 20910 +1(301)319-2032
-----Original Message----- From: Mike Panciera [mailto:notifications@github.com] Sent: Wednesday, July 22, 2015 11:33 AM To: VDBWRAIR/bio_pieces Cc: Maljkovic Berry, Irina CTR USARMY MEDCOM WRAIR (US) Subject: [bio_pieces] Identifying Genes with degenerate bases (#39)
As per discussion with @InaMBerry https://github.com/InaMBerry Given a FASTA file and either:
- annotation file for reference
- genbank id of reference
Output a full list of which genes degenerate bases occur in. I think we concluded that we would like an option to provide an annotation file as an option or provide the reference ID and fetch the annotation from GenBank.
Example Output: Gene1: R at position 300 Gene1: Y at position 500 Gene2: ....
or: Gene1 had 2 degenerate bases Gene2 had 1 degenerate bases
— Reply to this email directly or view it on GitHub https://github.com/VDBWRAIR/bio_pieces/issues/39 . https://github.com/notifications/beacon/AKlTHMjVUVVdeo0zB5XM4NfoRWzl1YVQks5of680gaJpZM4FdrSi.gif
Classification: UNCLASSIFIED Caveats: NONE
averagehat
necrolyte2
demis001
As per discussion with @InaMBerry Given a FASTA file and either:
Output a full list of which genes degenerate bases occur in. I think we concluded that we would like an option to provide an annotation file as an option or provide the reference ID and fetch the annotation from GenBank.
Example Output: Gene1: R at position 300 Gene1: Y at position 500 Gene2: ....
or: Gene1 had 2 degenerate bases Gene2 had 1 degenerate bases