Question: Sequences alignment program
0
gravatar for biancabernasconi
7 months ago by
biancabernasconi0 wrote:

Hello, which alignment program can I use to search for nucleotide sequences very similar to the query? Typically, place the sequence on the genome?

Is it Blast? But, which specific kind? Thank you.

alignment • 205 views
ADD COMMENTlink modified 7 months ago by onestop_data260 • written 7 months ago by biancabernasconi0

have you tried to literally search "which alignment program can I use to search for nucleotide sequences very similar to the query" in google.

that first result seems promising. (and then have a look in the tool manual)

ADD REPLYlink written 7 months ago by lieven.sterck8.5k

Some alignment tools do better than others, depending on sequence length and content. Can you describe a little more about the characteristics of what you're querying? That might help give you a more specific recommendation.

ADD REPLYlink written 7 months ago by Alex Reynolds30k
1
gravatar for genomax
7 months ago by
genomax89k
United States
genomax89k wrote:

You could use blat instead of BLAST+. You can find more info and executables from Jim Kent at UCSC.

ADD COMMENTlink written 7 months ago by genomax89k
1
gravatar for Alex Reynolds
7 months ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

Depending on the length of what you're querying, there may be other tools worth considering for shorter sequence queries, in addition to blat (especially if working with sequences less than 20nt long).

BLAST's blastn has a blastn-short argument that may be useful here. Bowtie is another option, and Bowtie 1 may be better (more accurate) than Bowtie 2 for this task, for instance; see: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

If you want to investigate the command-line version of UCSC blat, I put together a write-up that explains how to compile it, how to create a filter for speeding up queries, and an example of how to query: http://www.bitsumma.com/2017/09/03/how-to-install-and-set-up-a-local-ucsc-blat-environment/

ADD COMMENTlink written 7 months ago by Alex Reynolds30k
0
gravatar for onestop_data
7 months ago by
onestop_data260
onestop_data260 wrote:

It depends a lot on your query and database and how much memory you have available.

I wrote this blog post about BLAST and some faster alternatives depending on some conditions.

ADD COMMENTlink written 7 months ago by onestop_data260
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