Question: sense versus antisense (plus or minus) sequence alignment
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gravatar for a.alsayed.phd
9 months ago by
a.alsayed.phd10 wrote:

Please, if I have a couple of query (parts of virus genome) sequences and a couple of references sequences, what are the steps required to align them correctly;i.e, to ensure that I alighn sense with sense etc. (the same direction)?

Many Thanks

ADD COMMENTlink modified 9 months ago • written 9 months ago by a.alsayed.phd10
1

What are exactly "parts of virus genome"? RNAseq reads? An assembled virus transcriptome? Could you provide more details?

ADD REPLYlink written 9 months ago by h.mon15k

DNA seqs reads - sanger sequencing of PCR products

viral capsid regions (VPs) of human rhinoviruses

ADD REPLYlink written 9 months ago by a.alsayed.phd10

All sequence aligners check both orientations when doing alignments.

ADD REPLYlink written 9 months ago by genomax49k
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