Method(s) that from a BLASTp, and from the HSP protein accessions, retrieve the GBK record for each accession. Additionally, a FASTA file containing all HSPs can be output if desired.
- BioPython Modules
- Blast
- Entrez
- SeqIO
Several Parts:
-
Fetch FASTA file based on desired protein for BLASTp
-
Run BLASTp with fetched FASTA file
-
Parse BLASTp Results
-
IDentify "best" method from GBK file retrieval
a) esearch
b) elink
c) efetch
-
FASTA export (if desired)
- Mostly the same as the
retrieveGBK.py
script; but contains more notes and description than the script.