Not able to retrieve PDB id from standalone blast against PDB
0
0
Entering edit mode
9.2 years ago

I setup blast against nr database/pdb (downloaded from ncbi) and I want to extract PDB id from my blast results. I used various tags from blast output format but in some entries I am not Getting PDB id.

sample of results:

gi|349951|pdb|3YPI|A            gi|349951|pdb|3YPI|A;gi|349952|pdb|3YPI|B                 349951      349951;349952                                             3YPI_A        3YPI_A          3YPI_A;3YPI_B
gi|6320255|ref|NP_010335.1|     gi|6320255|ref|NP_010335.1|;gi|136069|sp|P00942.2|...     6320255     6320255;136069;798902;1197083;45269201;151942040;1...     NP_010335     NP_010335.1     NP_010335;P00942;CAA89080;AAA88757;AAS55980;EDN603...

In first output PDB id is 3YPI. but no Pdb Id in second one. why? (I am running blast against pdb db)

Is nr db is different from PDB db?

blast • 2.3k views
ADD COMMENT
0
Entering edit mode

question not tool please.

ADD REPLY

Login before adding your answer.

Traffic: 2934 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6