Blast Search PDB
Blast Protein Data Bank for structures matching a user given sequence.
-
prody_blast(sequence, **kwargs)[source]
Blast search PDB and download hits.
| Parameters: |
- sequence – sequence or file in fasta format
- identity (float) – percent sequence identity for blast search, default is 90.0
- overlap (float) – percent sequence overlap between sequences, default is 90.0
- outdir (str) – download uncompressed PDB files to given directory
- gzip – write compressed PDB file
|
|---|
Blast Parameters
| Parameters: |
- filename (str) – a filename to save the results in XML format
- hitlist_size (int) – search parameters, default is 250
- expect (float) – search parameters, default is 1e-10
- sleep (int) – how long to wait to reconnect for results, default is 2
sleep time is doubled when results are not ready.
- timeout (int) – when to give up waiting for results. default is 30
|
|---|