Obtaining the top matches from blast

Question

[S]

Hi,

I have downloaded the current version of the stand-alone-blast (ncbi-blast-2.2.29+) and I am trying to use blast (blastn) to find similarity of of a group of nucleotide sequences that I have. However, I am interested on only the top 3 matches. I tried searching online and I saw some posts that suggests using -K, but I realized this does not work with the new version that I am using. I looked at the help document and I tried using (-max_target_seqs) and (-num_alignments) but none of them worked. The result contains all the matches found by blast.

Does anyone know how to limit the results to let say just top 3 matches?

Thanks!

[sinhaurjoshi]

Could you plz explain a bit more about the sorting technique that has been referred to in this thread?

Answer 1

[hpmcwill]

Depends what you are trying to do.

As Neilfws says, if you want to limit the number of hits reported you can use (from the NCBI BLAST+ help output):

 -num_descriptions <Integer, >=0>
   Number of database sequences to show one-line descriptions for
   Not applicable for outfmt > 4
   Default = `500'
    * Incompatible with:  max_target_seqs
 -num_alignments <Integer, >=0>
   Number of database sequences to show alignments for
   Default = `250'
    * Incompatible with:  max_target_seqs

These correspond to the '-v' and '-b' options in legacy NCBI BLAST:

  -v  Number of database sequences to show one-line descriptions for (V) [Integer]
    default = 500
  -b  Number of database sequence to show alignments for (B) [Integer]
    default = 250

The '-K' option in legacy NCBI BLAST:

  -K  Number of best hits from a region to keep. Off by default.
If used a value of 100 is recommended.  Very high values of -v or -b is also suggested [Integer]

Is slightly different and maps to the '-culling_limit' parameter in NCBI BLAST+:

 -culling_limit <Integer, >=0>
   If the query range of a hit is enveloped by that of at least this many
   higher-scoring hits, delete the hit
    * Incompatible with:  best_hit_overhang, best_hit_score_edge

You may also want to limit the number of matches reported per hit (i.e. limit the number of HSPs):

 -max_hsps <Integer, >=0>
   Set maximum number of HSPs per subject sequence to save (0 means no limit)
   Default = `0'

For more information about the NCBI BLAST+ command-line options see:

• NCBI BLAST+ usage/help output (run the relevant BLAST program with the '-help' option)
• BLAST Command Line Applications User Manual
• NCBI's BLAST help

[S]

Thank you very much hpmcwill! I am sorry that my post was not clear enough, I was looking to limit the number of matches reported per hit so (-max_hsps) did the job.

Answer 2

[shinken123]

Using the output of blast using the option -outfmt 6

What about:

awk '!seen[$1]++' Blast_output_file.txt > Besthit_Blast_output_file.txt

[florian.grosmaire]

Hello,

Could you explain your awk command please ? I am very interested by it !

Answer 3

[Neilfws]

The relevant options are in the BLAST handbook:

num_descriptions    integer 500 Show one-line descriptions for this number of database sequences.
num_alignments  integer 250 Show alignments for this number of database sequences.

[S]

Thank you very much for the link!

Answer 4

[edrezen]

Hi,

What is the output format you use ? I think these options may not work with the default blast output format.

If you try the tabular output format (just add -outfmt 6 to your command), it may work better.

[S]

Changing the format to option 6 didn't help.

Answer 5

[Whoknows]

Hi

Please run your query with this parameter -outfmt 6 with this you can select those with highest similarity and also you can find out the number of mismatches, Then sort it .

But use this -best_hit_overhang for finding best hit over the blast.

[S]

Hi,

Thanks for the response. I knew I could sort and pick the top hit but I just thought there should be a parameter while running blast that can limit the results (at least there was one for an older version).

Thanks!