4 ms·

OP here. We've been working on faster bioinformatics algorithms for the past year – this is a demo of one application which is effectively a fast replacement fo

by nkrumm 12y ago

OP here. We'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.

hrjet 12y ago
Once upon a time, I had briefly looked at gene matching algorithms like FASTA. n00b question: Can these algorithms be generalized to any code (not just genetic codes). For example, to match Java bytecode, or x86 op-codes.
- sakai 12y ago
  In principle, some of them can be yes. Though genetic reference datasets tend to be much larger than, e.g., codebases -- and therefore require different approaches. One of the core things we're working on is a data structure for more efficient, constant-time sequence lookups, and we've definitely thought of some non-bioinformatics use cases as well. Happy to answer any more specific questions by email too (in my profile)!
  - infinite8s 12y ago
    Wouldn't some of the new timeseries motif searching approaches work in this domain (you could assume each codon is a quantized enumerated value). Something like iSax (http://www.cs.ucr.edu/~eamonn/iSAX/iSAX.html http://www.cs.ucr.edu/~eamonn/iSAX/iSAX.html) or Dynamic Time Warping (for motifs that are noisy) - http://www.cs.ucr.edu/~eamonn/SIGKDD_trillion.pdf http://www.cs.ucr.edu/~eamonn/SIGKDD_trillion.pdf
kevinwuhoo 12y ago
This is really cool. I'd really love to set this up for use in the lab I work with. Are you guys planning on releasing a binary or web interface where I can upload my own *omic data for searching?
- sakai 12y ago
  Hope it was clear that you can test it out with some small FASTA or FASTQ files now (just drag onto the upload icon). And yes, we'd be happy to discuss your use case and get you set up with something. Just shoot me a note at nick at helix dot io and we can follow up off thread.

by nkrumm 12y ago

hrjet 12y ago

Once upon a time, I had briefly looked at gene matching algorithms like FASTA. n00b question: Can these algorithms be generalized to any code (not just genetic codes). For example, to match Java bytecode, or x86 op-codes.

sakai 12y ago
In principle, some of them can be yes. Though genetic reference datasets tend to be much larger than, e.g., codebases -- and therefore require different approaches. One of the core things we're working on is a data structure for more efficient, constant-time sequence lookups, and we've definitely thought of some non-bioinformatics use cases as well. Happy to answer any more specific questions by email too (in my profile)!
- infinite8s 12y ago
  Wouldn't some of the new timeseries motif searching approaches work in this domain (you could assume each codon is a quantized enumerated value). Something like iSax (http://www.cs.ucr.edu/~eamonn/iSAX/iSAX.html http://www.cs.ucr.edu/~eamonn/iSAX/iSAX.html) or Dynamic Time Warping (for motifs that are noisy) - http://www.cs.ucr.edu/~eamonn/SIGKDD_trillion.pdf http://www.cs.ucr.edu/~eamonn/SIGKDD_trillion.pdf

kevinwuhoo 12y ago

This is really cool. I'd really love to set this up for use in the lab I work with. Are you guys planning on releasing a binary or web interface where I can upload my own *omic data for searching?

sakai 12y ago
Hope it was clear that you can test it out with some small FASTA or FASTQ files now (just drag onto the upload icon). And yes, we'd be happy to discuss your use case and get you set up with something. Just shoot me a note at nick at helix dot io and we can follow up off thread.