Find The Rid For A Remote Blast+ Result

Question

[Behindtherabbit]

I ran a remote blastn search using the command line blast 2.2.25+ and got the results back in asn format. when I went to reformat the results using blast_formatter, I realized I needed the RID for my search - and I can't find it anywhere.

does a remote commandline blast search return you the RID? if so, where would I find it?

thanks for any help!

Answer 1

[vijay]

As far as I know, the command line BLAST output results does not contain your RID. RID is a key that is assigned automatically to your search result each time you run a online BLAST. It is used to identify your search results from the BLAST server at a later point of time. Please correct me if I am wrong.

[Behindtherabbit]

well, I fear you may be right - but that's frustrating because it was touted as an improvement over the old way of running remote blast searches. :-@

Answer 2

[Behindtherabbit]

among other mentions of blast+, the -remote flag, and RIDs on the Web, I found this tantalizing comment from Feb 2012:

The BLAST+ remote service can submit multiple queries (from FASTA input) at once, poll for the results using the BLAST RID, and also print the RID in the BLAST report.

which seems to suggest it is possible.

[Hamish]

The plain text forms of the BLAST output contain the RID when invoked with the -remote flag (or when run via the BLAST APIs provided by NCBI).

Answer 3

[Fwip]

Have you tried using the command blast_formatter -archive yourfile.asn? It seems like it's an alternative to using the RID.

Answer 4

[Behindtherabbit]

yes, blast_formatter -archive file.asn works when an archive has been created via local blast (i.e., when the blast database is local). it fails when I run command line blast in conjunction with the -remote flag, reporting that it needs the RID. I assume that blast -remote ... does not return some necessary info required to re-format the results, but that is just an assumption.

for example:

blastn -task megablast -outfmt 11 -db nt -query my_qfile.fa -out my_arch.asn -remote

I get a valid asn file.

blast_formatter -archive my_arch.asn -outfmt "6 qseqid sseqid qlen slen length pident qstart qend sstart send evalue mismatch gaps bitscore" -out my_table.txt

it fails, asking for the RID.

if I remove the -remote flag, the formatting works - but I'd rather avoid keeping a synched local copy of nt on my laptop. call me crazy. :-D

[Hamish]

The -remote flag runs the BLAST on the NCBI's servers, were the archive format will be produced an retained for use when retrieving the result, this means you can do:

$ blastp -db nr -query prot_uniprot_1A112_ARATH.tfa -out blah.blast.txt -remote
$ grep 'RID:' blah.blast.txt
RID: ZMWGVXS8014
$ blast_formatter -rid ZMWGVXS8014 -outfmt 6

Note: some of the BLAST output formats do not have anywhere for the RID to be placed without breaking the output format, so for the initial search be sure to use a format which will contain the RID. This means your initial search needs to use one of:

• 0 = pairwise. RID is part of the header block.
• 1 = query-anchored showing identities. RID is part of the header block.
• 2 = query-anchored no identities. RID is part of the header block.
• 3 = flat query-anchored, show identities. RID is part of the header block.
• 4 = flat query-anchored, no identities. RID is part of the header block.
• 7 = tabular with comment lines. RID appears in a header comment.

So you can get hold of the RID in order to request alternative formats.