cannot get usearch ublast to work for nucleotide

rv20

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Join Date: Nov 2015

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cannot get usearch ublast to work for nucleotide

04-17-2016, 10:56 AM

Hi Everyone,
I am having some trouble using usearch ublast. I am trying test a database I made using:

usearch -makeudb_ublast myFasta.fasta -output db.udb -alpha nt

I used a sequence that should return hits, but usearch ublast says that 0.0% matched. The command I am currently using is:

usearch -ublast query.fasta -db db.udb -strand both -evalue 1e-5 -alnout output.aln

I have tried using different combinations of -evalue and -strand and I have double checked that I am using the command correctly.

Also I made databases with makeblastdb, and tests for those returned the proper results when I used the same sequences as in usearch.

I am using usearch v8.1.1861

Can anyone figure out what I am doing wrong?
Tags: bioinformatics, blast, nucleotide, ublast, usearch

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