Show HN: Helix I/O – Ultrafast genomic search

This looks neat, but is the method open? Is there a command line version?<p>I&#x27;d argue that while open source is a desirable feature in most software, it&#x27;s a <i>necessary</i> feature in scientific software. When our results depend on running through software, that software can&#x27;t be a proprietary, closed-source black box.

OP here. We&#x27;ve been working on faster bioinformatics algorithms for the past year – this is a demo of one application which is effectively a fast replacement for BLAST. Happy to answer any questions about tech or usage.

We help use the NMPDR RAST servers and also run our own for sequence annotation. I&#x27;d have to check but if I&#x27;m remembering correctly our annotations fix errors (~%5) present in the NCBI databases and catches many more (something like ~20% of unknowns) for the organisms we work with. Problem is searching our indexes is super slow (comparatively) and not all in one place -- BLASTn&#x2F;p takes some fiddling.<p>Could we use our own corpus for this?<p>Ah, I see you have some problems with species identification...are you using old NCBI datasets?<p>(ps. If you&#x27;d like to talk, you can email me at the address in my profile)

This is very cool. I love data, all kinds of data. The more data we have available, the better.<p>But... what&#x27;s the use case for this? Are there people with genomic sequences just laying around with no idea of what they represent? Or is it a resource for students?<p>(Serious question.)

Hi and congratulations, this looks like an excellent tool for bioinformatics. Just out of curiosity, how can you mathematically guarantee constant time searches independent of the database size?

What stack are you using? Are you using anything like elasticsearch or non-sql Dbs ?

Would be a lot more fun if it had eukaryotes.