Question: Not able to retrieve PDB id from standalone blast against PDB
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gravatar for thind.amarinder
4.1 years ago by
Italy
thind.amarinder10 wrote:

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 • 1.2k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 4.1 years ago by thind.amarinder10

question not tool please.

ADD REPLYlink written 4.1 years ago by dago2.5k
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