Generate pin phr and psq files of a fasta file

Question

[Natasha]

Hi All,

I have downloaded a fasta from UniprotKB. I would like to use this file for protein identification but the identification step in OpenMS also requires .pin, .phr, .psq files of the relevant fasta file. I am not sure how to generate these files.

Could someone please help me with this?

The fasta file that I have is uploaded here

[lieven.sterck]

no idea what that openMS is but those file extensions hint towards blast-DB formatted files.

You could thus, if that makes sense for that tool, get those by making a blastDB from your fasta file (makeblastdb cmd)

[Natasha]

Hi, thanks for the suggestion. I'm sorry for the naive question, I'm new to this. Could you please let me know which package has to be installed to use this command?

[lieven.sterck]

sure, you'll need the blast package (NCBI blast) to be installed.

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download

[Natasha]

Hi, I tried

X:\Program Files\NCBI\blast-BLAST_VERSION+\bin
λ makeblastdb -in uniprot.fasta

I am not sure what are other arguments have to be specified. Could you please have a look?

USAGE

  makeblastdb [-h] [-help] [-in input_file] [-input_type type]
    -dbtype molecule_type [-title database_title] [-parse_seqids]
    [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids]
    [-mask_desc mask_algo_descriptions] [-gi_mask]
    [-gi_mask_name gi_based_mask_names] [-out database_name]
    [-blastdb_version version] [-max_file_sz number_of_bytes]
    [-metadata_output_prefix ] [-logfile File_Name] [-taxid TaxID]
    [-taxid_map TaxIDMapFile] [-version]

DESCRIPTION
   Application to create BLAST databases, version 2.13.0+

Use '-help' to print detailed descriptions of command line arguments
========================================================================

Error: Argument "dbtype". Mandatory value is missing:  `String, `nucl', `prot''
Error:  (CArgException::eNoArg) Argument "dbtype". Mandatory value is missing:  `String, `nucl', `prot''

[lieven.sterck]

well, as the message says you need to specify the -dbtype argument on your cdmline (it will be prot given the extensions you mentioned, this means you want to format a DB containing protein sequences)

[Natasha]

λ makeblastdb -in uniprot.fasta -out uniprot -dbtype prot -title "uniprot" -parse_seqids


Building a new DB, current time: 04/04/2022 16:52:32
New DB name:   C:\Program Files\NCBI\blast-BLAST_VERSION+\bin\uniprot
New DB title:  uniprot
Sequence type: Protein
Keep MBits: T
Maximum file size: 3000000000B

No volumes were created.

Error: mdb_env_open: Input/output error

Thanks so much, I get the above error this time. I'm not sure if I have missed something. Could you please have a look?

[lieven.sterck]

can't tell remotely :/

there are a number of things to check though:

• is the location where you want to put (the -out parameter) the output files of this writable for you?
• is the input fasta file correctly formatted?

[Natasha]

I didn't run a command that does the formatting.

From what's described here https://cgpdb.ucdavis.edu/BlastParser/Blast_Parser.html

First format the database file. Type in the following command:

formatdb -i NB-ARC.fasta -p T

but I am not sure where to find formatdb. This is not available in the bin folder of the blast package which I have downloaded. Instead of formatdb, blast_formatter is available. But the input arguments are different (I don't find T). Not sure how to format the fasta file.

[lieven.sterck]

those are the old NBCI blast versions (< 2.10.1 ) , perhaps you need those but then you'll have to download a blast version of a couple of years old, those still have the formatdb etc .

In the new version those have been replaced with makeblastdb

[Natasha]

Ahh, my mistake. It wasn't writable. Thanks so much. This works