This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Generate pin phr and psq files of a fasta file

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

openms proteomics knime fasta uniprot
• 3,542 views • link
updated by lieven.sterck lieven.sterck • written by Natasha • Natasha

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)

• 0 views • link
written by lieven.sterck lieven.sterck

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?

• 0 views • link
written by Natasha • 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''
• 0 views • link
written by Natasha • Natasha

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)

• 0 views • link
written by lieven.sterck lieven.sterck 
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?

• 0 views • link
written by Natasha • Natasha

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?
• 0 views • link
written by lieven.sterck lieven.sterck

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.

• 0 views • link
written by Natasha • Natasha

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

• 0 views • link
written by lieven.sterck lieven.sterck

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

• 0 views • link
written by Natasha • Natasha

0 answers

No answers yet.

Log in to answer this question.

More posts like this