Work

Frag Gene Scan HPC

HPC
C
MPI

Acceleration of a gene prediction method on multicore clusters.

Gene Chain

Gene prediction mechanisms are part of the field of computational biology and are used to identify fragments of sequences (usually DNA) that are biologically functional (for example, identify those genes that encode proteins).

Gene identification is one of the first and most important steps to understand the genome of a species once it has been sequenced.

The FragGeneScan[1] tool allows do predictions of genes in current metagenomic projects, such as the human genome.

FragGeneScan is capable of obtain a high precision, especially in large data sets with many short sequences. However, it has the drawback of requiring a very long computing time.

The objective of this work will be the development of a hybrid parallel application (with threads and MPI processes) that exploits the computational capacity of multicore system clusters to accelerate gene prediction.

The output of this tool must be the same as that of FragGeneScan in order to guarantee the correctness of the results.