The Same Sequence Occurs Multiple Times In Blastp Output

Question

[Janne Marie Laursen]

Hi there,

I am using blastp (using blast+ 2.2.25) to align bacterial proteins (in the file multiple_queries.fasta) against a custom database (genome.db) containing all proteins coded by the genomes of 6 different bacteria.

I used the following command:

blastp -query multiple_queries.fasta -db genome_db -out file_out.txt -outfmt "6 qseqid sseqid evalue bitscore qlen slen length pident ppos gaps" -num_alignments 50

Some of the output in file_out.txt looks like this for the query P21171:

...
P21171 gi|16804543|ref|NP_466028.1| 6e-50 194 484 401 141 64.54 74.47 8
P21171 gi|16802439|ref|NP_463924.1| 6e-35 144 484 227 119 57.14 75.63 3
P21171 gi|16802439|ref|NP_463924.1| 0.006 38.5 484 227 80 36.25 47.50 3
P21171 gi|126697942|ref|YP_001086839.1| 5e-26 115 484 335 125 49.60 67.20 6
P21171 gi|126698969|ref|YP_001087866.1| 2e-25 113 484 509 105 46.67 64.76 2
...

I am puzzled by line 2 and 3 in this output.
When I ran the same query protein (P21171) on the blastp web-interface, I didn't get these unusual hits. I don't understand why blastp gives two different results for the same sequence.

Thanks for your time!

Answer 1

[Michael Kuhn]

Please try running it in normal output format (i.e. human-readable with alignments) . You'll probably find that there are two hits at different ends of the subject protein, with some intervening sequence that BLAST didn't align.

[Janne Marie Laursen]

Right you are - thanks! I got two alignments (one in each end of the protein). Do you happen to know how it is possible to print only the best hit for each sequence?

[Michael Kuhn]

AFAIK this is not possible

[Neilfws]

Enter the BLAST parser :)

[Neilfws]

That's why we have BLAST parsers.

[Janne Marie Laursen]

I couldn't find anything in the manual either. Thanks again.