iten

3 ms·

1. 1.▲
   by iten 3y ago

   Small correction: BLAT is a local alignment tool Jim Kent also wrote. I think his assembler you're referring to is GigAssembler ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311095/ ).
2. 2.▲
   by iten 5y ago

   The author makes a critical mistake when analyzing the BNT/Pfizer clinical trial. Over and over when discussing the results they mention calculating efficacy against "infections" using this data. But this specific clinical tr
3. 3.▲
   by iten 7y ago

   I recently completed my PhD in vertebrate comparative genomics so this is fun to see. The single most important factor that needs to be accounted for in analyses like these is the correlation between phylogenetic similarity and the trait in
4. 4.▲
   by iten 8y ago

   We use KT's in-memory database in a scientific computing application I work on (to store a graph 30-100GB in size accessed by 100-1000 workers). The performance is very impressive, and it's been reliable for our use case. But I do
5. 5.▲
   by iten 12y ago

   To be fair, to my knowledge, LASTZ, BLAST, or BLAT don't treat IUPAC ambiguous bases (K, Y, R, etc.) in the way the OP was looking for. That's not to blame the tools, since they have a very good reason not to (they build an inde
6. 6.▲
   by iten 12y ago

   What proportion of bases in your query were ambiguous? If it was a fairly low percentage (~10-20%?), I think you could probably get away with using LASTZ, treating all ambiguous bases as completely ambiguous (--ambiguous=iupac), then writ