2 ms·

This is very cool. I love data, all kinds of data. The more data we have available, the better. But... what's the use case for this? Are there people with geno

This is very cool. I love data, all kinds of data. The more data we have available, the better. But... what's the use case for this? Are there people with genomic sequences just laying around with no idea of what they represent? Or is it a resource for students? (Serious question.)

nkrumm 12y ago
Good question. We're targeting analysis of "next generation" DNA sequencing data, as is commonly applied in research settings today. Clinicians and researches are beginning to use sequencing to try and identify bacteria, viruses or other organisms in complex samples (either from patients or from environmental samples). These complex “metagenomic” samples can be processed using our tool (we've set up a demo on the submitted link), in order to understand a sample's composition, or to see if there are relevant pathogens in the sample.
cfontes 12y ago
If I got the tool right, one use case would be similarity search. So you just finished the brand new genome sequencing of Sugarcane for example. And you are interested in Aluminium resistence genes to be able to plant sugarcane in aluminium packed soils that would normally kill the plant. What you do is to throw parts of the genome in a tool like that (there are others) and see if you can find a match for a Sorghum(Wheat,Corn...) Aluminium resistence gene that has been already researched and tested. The closest related the better. Now you have some clue about where to start your studies or which genes you should be looking for in your new varieties or which gene to try to insert in your next Agrobacterium or gene bombardment test. Cheers. PS: I left the Bioinformatics field a few years ago (best job I ever had BTW) So correct me if I am wrong.
- sakai 12y ago
  cfontes – Yes, that's definitely another use case of the underlying technology, though please note that the database loaded for the demo only include archaeal, bacterial and viral genomes (so you'd have a very hard time getting a hit on sugarcane sequences!). (This is nkrumm's and my project)
  - cfontes 12y ago
    Nice... Thanks for the explanation and good luck.

nkrumm 12y ago

Good question. We're targeting analysis of "next generation" DNA sequencing data, as is commonly applied in research settings today. Clinicians and researches are beginning to use sequencing to try and identify bacteria, viruses or other organisms in complex samples (either from patients or from environmental samples). These complex “metagenomic” samples can be processed using our tool (we've set up a demo on the submitted link), in order to understand a sample's composition, or to see if there are relevant pathogens in the sample.

cfontes 12y ago

If I got the tool right, one use case would be similarity search. So you just finished the brand new genome sequencing of Sugarcane for example. And you are interested in Aluminium resistence genes to be able to plant sugarcane in aluminium packed soils that would normally kill the plant. What you do is to throw parts of the genome in a tool like that (there are others) and see if you can find a match for a Sorghum(Wheat,Corn...) Aluminium resistence gene that has been already researched and tested. The closest related the better. Now you have some clue about where to start your studies or which genes you should be looking for in your new varieties or which gene to try to insert in your next Agrobacterium or gene bombardment test. Cheers. PS: I left the Bioinformatics field a few years ago (best job I ever had BTW) So correct me if I am wrong.

sakai 12y ago
cfontes – Yes, that's definitely another use case of the underlying technology, though please note that the database loaded for the demo only include archaeal, bacterial and viral genomes (so you'd have a very hard time getting a hit on sugarcane sequences!). (This is nkrumm's and my project)
- cfontes 12y ago
  Nice... Thanks for the explanation and good luck.