Re: [boost] Genetics library: Volunteers needed

Subject: Re: [boost] Genetics library: Volunteers needed
From: Paul A. Bristow (pbristow_at_[hidden])
Date: 2015-07-21 09:42:50

> -----Original Message-----
> From: Boost [mailto:boost-bounces_at_[hidden]] On Behalf Of Andy Thomason
> Sent: 21 July 2015 13:11
> To: boost_at_[hidden]
> Subject: [boost] Genetics library: Volunteers needed
> 
> Hi All,
> 
> I am recruiting users for the putative genetics library.
> 
> https://github.com/andy-thomason/genetics
> 
> We have a few simple examples of gene searching and I am working on a more complete aligner
> example and some performance improvements to the index data structure.
> 
> For data, you can obtain the human genome from:
> 
> ftp://ftp.ensembl.org/pub/release-
> 81/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
> 
> Interesting problems we would like to solve:
> 
> Given a 20 character sequence with up to six errors, what is the fastest way to list all
possibilities
> other than a brute force search (CRISPR).
> 
> Can we use JNI to connect the library to Hadoop and other distributed seach systems?
> 
> Can we construct a database of all known viral genomes including recombination?
> 
> Can we detect variations in MHC VDJ regions within a single sample?
> 
> Many other interesting puzzles are there to be found...
> 
> Andy.

Potential users may find the draft docs useful at

https://rawgit.com/andy-thomason/genetics/master/doc/html/index.html

(if lacking some icons and style sheets to see in all their glory ;-)