[boost] Genetics library: Volunteers needed

Subject: [boost] Genetics library: Volunteers needed
From: Andy Thomason (a.thomason_at_[hidden])
Date: 2015-07-21 08:11:14

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.

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