How can I retrieve the Protein 'name' using my BLAST tab delimited results?

Question

[Tawny]

I have a file of BLAST protein results. It is over 100000 lines long. I want to get the protein/gene title associated with each accession number. I have been looking for a file I could search through similar to gene2refseq that would have the protein title mapped to the GI or accession with no luck.

I have tried to figure out how to use Bio::DB::EUtilities to retrieve what I need but I don't know what method to use that will get what I want back.

For example, using protein accession WP_009600323.1 I want to get back tRNA uridine(34) 5-carboxymethylaminomethyl synthesis enzyme MnmG [Vibrio caribbeanicus].

How can I get this information? Thank you.

[5heikki]

In case you're blasting against some prebuilt NCBI blast db, you could have:

-outfmt '6 std stitle'

or

-outfmt '6 std salltitles'

But only suckers read things like manuals or output of:

command -h
command -help
man command

Right?

Anyway, you don't have to re-blast (assuming prebuilt NCBI blast db):

blastdbcmd -help

[GenoMax]

Let us give @Tawny the benefit of doubt.
As @5heikki said you can use blastdbcmd (a command line utility from blast+ package) to get the info you need. blastdbcmd -db /path_to/nr -entry WP_009600323.1 -outfmt "%t"
Check blastdbcmd -help to investigate -entry_batch option that would allow you to provide a file with these ID's and get all results back at once.

[Tawny]

Both @5heikki and @genomax2 are correct. If the -outfmt stitle had been used my problem would have already been solved. BLAST+ can give me what I need. But in this instance I do not have the database that was used to generate this BLAST output. I am running the blastdbcmd using a database that I have that should be close to what was used to generate my data but it is not 100% complete. I am getting a very large number of OID not found errors. What other method can be used to get the protein title?

[GenoMax]

Did you try nr? If ID's are not there in nr then perhaps it some may have been retired (perhaps duplicates).

[5heikki]

With Entrez Direct something like:

efetch -db protein -id WP_009600323.1 -format xml \
| xtract -element Prot-ref_name_E -element Org-ref_taxname \
| awk 'BEGIN{FS="\t"}{print $1" ["$2"]"}'
tRNA uridine(34) 5-carboxymethylaminomethyl synthesis enzyme MnmG [Vibrio caribbeanicus]

Not sure it's the same elements for all accessions. It's easier with gi number:

efetch -db protein -id 497286106 -format docsum | xtract -element Title
tRNA uridine(34) 5-carboxymethylaminomethyl synthesis enzyme MnmG [Vibrio caribbeanicus]

It's sad how the NCBI is phasing out gi numbers, while so many of their services (including standalone blast) still can't provide the same level of convenience with accessions..

[Tawny]

@5heikki thank you for the efetch command. I am just getting back to this problem after working on some other projects. I was able to include the second efetch command you posted into a Perl script and it is working nicely. It is slow but does the job.

Answer 1

[DCGenomics]

This should work:

cat file_of_accessions | epost -db protein -format acc | efetch -format docsum | xtract -pattern DocumentSummary -element AccessionVersion Title