EMBOSS Primersearch qualifiers

Question

[johndoe]

Hi,

According to the manual primersearch from EMBOSS allows the use of -Iquery as a qualifier.

I essentially only want to search a part of my sequence file with my primer list based on sequence name. A couple of weeks ago I did this and was able to only look for hits from a certain sequence. Now I started playing around with my pipeline again and although I don't need the function as I can analyze afterwards, it would cut down on the time spent running primersearch on my data set.

Anybody have an idea how I would go about doing this, since I'm running primersearch over and over again it would help with the number of calculations done it I could cut down on the number of sequences being analyzed.

Thanks in Advance, Dave

[GenoMax]

I am not sure what exactly you are asking. If you don't want to use -iquery1 can you not just omit that option?

[johndoe]

I have an sequence file containing several different assemblies, I would like to use primersearch to search only one assembly, to save me computing time. I did this two weeks ago but have forgotten how. I don't want to split up the sequence file, because I'd like to use it will all assemblies later in the script I'm writing. I think it was iquery that I used to do this, but am not sure. Does anyone know how to use the EMBOSS qualifiers? Thanks, Dave

[Ram]

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