Expresso/3Dcoffee with local pdb database

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Esteban López Tavera

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Aug 19, 2022, 4:23:57 AMAug 19
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Dear T-coffee team,

I would like to run expresso relying only on a set of pdb files that I have (approx. 150), to align a set of ~1200 sequences. I would like to avoid t-coffee trying to fetch 

My guess is I need to run expresso (if I don't want to build a template file myself) and:
 - Build a file that can be the input to the option -pdb_db from my set of pdb files.
 - Input all the pdb files with the -pdb option.

My questions are:
 - How should the -pdb_db input look like? Any advice on how to build it?
 - Is there a way of inputting all the pdb files at once instead of individually?

Thanks in advance for your help.

Best,
Esteban

Athanasios Baltzis

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Aug 19, 2022, 4:52:35 AMAug 19
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Dear Esteban,

If I understand it correctly, you want expresso to search locally for templates only on this set of pdb files.

If this is the case, then you have to create a local blast-able sequence database from this set of pdb files and run the following command:

t_coffee <QUERY_FASTA> -mode expresso -blast=LOCAL -pdb_db=<PDB_DB_PATH - e.g. $HOME/db/myset.fasta> -pdb_type d -pdb_min_sim 95 -pdb_min cov 90

Kind regards,
Athanasios Baltzis
PhD Fellow in Bioinformatics | Data scientist
Notredame's lab - Comparative Bioinformatics Group
Centre for Genomic Regulation (CRG), Barcelona (Spain)
  


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Esteban López Tavera

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Aug 19, 2022, 7:28:31 AMAug 19
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Thank you, Athanasios.

Yes, precisely.
So the pdb_db file is just a simple fasta with the sequences corresponding to my pdbs?
I will try it. Thanks!

Best,
Esteban

Athanasios Baltzis

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Aug 19, 2022, 7:37:21 AMAug 19
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It is a fasta file that points to a blast database. This might help you on how to make such a database: https://www.ncbi.nlm.nih.gov/books/NBK569841/

Best,
Athanasios Baltzis
PhD Fellow in Bioinformatics | Data scientist
Notredame's lab - Comparative Bioinformatics Group
Centre for Genomic Regulation (CRG), Barcelona (Spain)
  

Esteban López Tavera

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Aug 19, 2022, 7:44:47 AMAug 19
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All right, thanks!

I have also created that blast db as in the link you just shared. I assume then the fasta I give to pdb_db is the one from which I created the blastdb, and it all must be in the same directory so that t-coffee can so-to-say find the db. Is that right?

Best,
Esteban

Athanasios Baltzis

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Aug 19, 2022, 7:48:03 AMAug 19
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Yes, right.

Athanasios Baltzis
PhD Fellow in Bioinformatics | Data scientist
Notredame's lab - Comparative Bioinformatics Group
Centre for Genomic Regulation (CRG), Barcelona (Spain)
  

Esteban López Tavera

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Aug 19, 2022, 7:52:24 AMAug 19
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Great, thanks!
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