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So DNA is a long string, with certain identified parts that have meaning (code for something we know). What would a layman like myself need to get myself to a

by ericb 17y ago

So DNA is a long string, with certain identified parts that have meaning (code for something we know). What would a layman like myself need to get myself to a hello world program that could take an actual DNA string(file) as input and give a hello for the presence an actual known gene? Not code-wise, that's obvious. I'm asking where I could get a sample genome, information about a gene, fill in the gaps of my understanding, etc. Anyone know?

bbgm 17y ago
While not genome centric (it's genotype-based) Promethease is one example http://www.snpedia.com/index.php/Promethease http://www.snpedia.com/index.php/Promethease 23andme's software does a pretty good job. You can also use the UCSC genome browser although it probably as a learning curve for most. http://genome.ucsc.edu/ http://genome.ucsc.edu/ Honestly, I believe that people need to understand the biology, some depth of what genes are, and what SNPs are etc. It's important as molecular medicine becomes the norm (still some ways away).
yannis 17y ago
You can start with your favorite language by downloading a library, there is bioPerl, bioPython, bioRuby and even bioPHP! The libraries have all the routines to connect to public sources. The National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/nuccore/89889045?report=fasta&log$=seqview http://www.ncbi.nlm.nih.gov/nuccore/89889045?report=fasta&#3... has an enormous database and is all open source. The link I quoted lists the genome for a virus. I wrote a short program in JavaScript that did frequency analysis on the pairs. It took 30ms in Chrome. It is actually not all that difficult at a certain level of analysis. In my mind the big question is, how can we understand how it works? It is like giving you a binary for windows to reverse engineer it. My own question is; does my DNA makes me? If my grandkids have it on a memory stick (it can actually fit), would they be able to 're-construct' me in some form of virtual reality? A potential area for hackers to get involved in my opinion - is the potential of the Cloud. You can imagine say 10 million genomes stored out there at the not so distant future and distributed software analyzing it and indexing it and all the ethical and other problems that come from it.

by ericb 17y ago

bbgm 17y ago

While not genome centric (it's genotype-based) Promethease is one example http://www.snpedia.com/index.php/Promethease http://www.snpedia.com/index.php/Promethease 23andme's software does a pretty good job. You can also use the UCSC genome browser although it probably as a learning curve for most. http://genome.ucsc.edu/ http://genome.ucsc.edu/ Honestly, I believe that people need to understand the biology, some depth of what genes are, and what SNPs are etc. It's important as molecular medicine becomes the norm (still some ways away).

yannis 17y ago

You can start with your favorite language by downloading a library, there is bioPerl, bioPython, bioRuby and even bioPHP! The libraries have all the routines to connect to public sources. The National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/nuccore/89889045?report=fasta&log$=seqview http://www.ncbi.nlm.nih.gov/nuccore/89889045?report=fasta&#3... has an enormous database and is all open source. The link I quoted lists the genome for a virus. I wrote a short program in JavaScript that did frequency analysis on the pairs. It took 30ms in Chrome. It is actually not all that difficult at a certain level of analysis. In my mind the big question is, how can we understand how it works? It is like giving you a binary for windows to reverse engineer it. My own question is; does my DNA makes me? If my grandkids have it on a memory stick (it can actually fit), would they be able to 're-construct' me in some form of virtual reality? A potential area for hackers to get involved in my opinion - is the potential of the Cloud. You can imagine say 10 million genomes stored out there at the not so distant future and distributed software analyzing it and indexing it and all the ethical and other problems that come from it.