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.
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biancabernasconi •
3 answers
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/
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.
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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)
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.