tools to align DNA sequences against protein sequence
Hi all,
I need to map a bunch of fastq files consisting of DNA sequences (paired end reads) against pan-genome proteins. So I need to align DNA sequences against proteins sequences. I used DIAMOND (which was very fast and user friendy), however later on I figured out it does not support paired-end reads. So I am looking for another tool to do it. I thought BlastX could do the job for me, but I am not sure if it can handle paired end reads or not?
I would appreciate if anyone who has experience with Blast let me know if using BlastX is an appropriate way for this purpose or if there is any other tool that I can use.
Thanks
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Should not matter that DIAMOND does not handle paired end reads. You are not going to get a drastically different answer from using just one of the reads from the pair.
If you are looking for discordant alignments then you are better off using regular NGS aligners.
exonerate may be a good option.