Question

blast two protein by pdb id

0

Entering edit mode

2.5 years ago

iamsmor • 0

Hello everyone I am trying to blast two protein (PDB ID:6UFO, 4XMB) each other using python. I read guideline but ı am not condifident user for python programme. I need help for this process. I will be greatful for any kind of little help. Thank you.

BLAST PROTEIN PYTHON • 986 views

ADD COMMENT • link updated 2.5 years ago by Asaf 10k • written 2.5 years ago by iamsmor • 0

2

Entering edit mode

why python when you can use a shell script ?

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

because ı followed guidline for NCBI blast. Btw ı got only similarity results by script of python.I used blast search tool and get some list of protein but ı dont know how ı can connect results to pubchem compount (by e-link)

ADD REPLY • link 2.5 years ago by iamsmor • 0

score 1 · Answer 1 · 2022-06-07

1

Entering edit mode

2.5 years ago

Asaf 10k

The easiest way would be to use NCBI BLAST web interface, where you can simply check the box next to "Align two or more sequences" and just give the accession IDs as input: pdb|6UFO|A and pdb|4XMB|A (A is the chain)

ADD COMMENT • link 2.5 years ago by Asaf 10k

0

Entering edit mode

thank you ı used web interface already but ı could not set elink for puchem compounds.