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Posting on behalf of Hannah, since her new account is getting blocked from replying: hi! resident scientist at Benchling here! searching near-exact sequence ca
by joshma 10y ago
Posting on behalf of Hannah, since her new account is getting blocked from replying:
hi! resident scientist at Benchling here! searching near-exact sequence can be really useful! for example, sometimes i would like to find if any of my plasmid has a certain signal peptide, it would be so hard without this search algorithm because so many DNA sequences can be translated to the same signal peptide. it would be great if i could just paste the amino acids and i could identify which plasmids contain the signal peptide.
- daemonk 10y agoI see. I guess near exact match functionality would be great for plasmids where there is a custom sequence inserted. But wouldn't a pre-processing pipeline that either automates annotation of the plasmid based on commonly used motifs (m17 primers, t7, sp6 promoters, fluorescent protein sequences, antibiotic resistence...etc) or requiring the user to annotate their plasmid during submission be more ideal? I would imagine the more common use case is to search for these elements?
- mbreese 10y agoBlastx? Or are your motifs too short? I know you mention that this isn't a use case for blast, but it's simple to keep a private blast index to use for cases like this.