tools to align DNA sequences against protein sequence

Question

[Ana]

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

[Sishuo Wang]

exonerate may be a good option.

[GenoMax]

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.