Forum:Computation-Intesive Application in the field of bioinformatics

Question

[mostafa.hadadian]

Hello

I want to do research in the field of bioinformatics. I'm looking for computation-intensive applications that need speed up. For example, the sequence alignment (e.g. Smith-Waterman) needs to be run fast. I look for applications that needs to execute faster and I want to improve one of such applications.

I will be grateful if you help me with this.

Best regards

[h.mon]

With the ever-increasing volume of data being spit by sequencers / mass-spectrometers / whatevers, any application / task you can speed-up (or decrease memory usage, or decrease disk usage) will benefit and become more useful.

But to name one: blastp-like searches have been incredibly sped-up in recent years, but blastn-like searches are lagging behind by a large margin.

[lieven.sterck]

I'm fully with h.mon on this one.

Though some alternatives/ attempts have been proposed, there is still room for improvements in the field of fast BLAST searches (blastx, blastn,... ) . Aside from speed-up , also try to mimick the 'old' blast results as much as possible I would recommend

Answer 1

[jeremieauger]

With metagenomics (study of bacterial groups from an environment) using Whole Genome Shotgun (WGS sequencing) technologies, there is one computer intensive task, namely "de novo clustering". Generally done using De Bruijn graphs, the task consists of taking short sequencing reads and assembling them into larger contigs. This article compares some tools that accomplish this task, like RayMeta: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0169662

These days, a lot of metagenomics studies are done using 16S, but WGS is gaining in popularity with the lowering of prices of sequencing.