Search results for "Software suite"
showing 4 items of 4 documents
Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS
2016
Interaction between genes has become a major topic in quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex diseases. Due to the number of tests required for an exhaustive search in genome-wide association studies (GWAS), a large amount of computational power is required. In this paper, we present a hybrid architecture consisting of tightly interconnected CPUs, GPUs and FPGAs and a fine-tuned software suite to outperform other implementations in pairwise interaction analysis while consuming less than 300Watts and fitting into a standard desktop computer case.
CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment
2017
Next generation sequencing (NGS) technologies have enabled cheap, large-scale, and high-throughput production of short DNA sequence reads and thereby have promoted the explosive growth of data volume. Unfortunately, the produced reads are short and prone to contain errors that are incurred during sequencing cycles. Both large data volume and sequencing errors have complicated the mapping of NGS reads onto the reference genome and have motivated the development of various aligners for very short reads, typically less than 100 base pairs (bps) in length. As read length continues to increase, propelled by advances in NGS technologies, these longer reads tend to have higher sequencing error rat…
Evaluating protein structures determined by structural genomics consortia.
2006
Structural genomics projects are providing large quantities of new 3D structural data for proteins. To monitor the quality of these data, we have developed the protein structure validation software suite (PSVS), for assessment of protein structures generated by NMR or X-ray crystallographic methods. PSVS is broadly applicable for structure quality assessment in structural biology projects. The software integrates under a single interface analyses from several widely-used structure quality evaluation tools, including PROCHECK (Laskowski et al., J Appl Crystallog 1993;26:283-291), MolProbity (Lovell et al., Proteins 2003;50:437-450), Verify3D (Luthy et al., Nature 1992;356:83-85), ProsaII (Si…
A topology-constrained distance network algorithm for protein structure determination from NOESY data.
2005
This article formulates the multidi- mensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-con- strained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology-constrained distance net- work analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DY- ANA. The minimum input for AutoStructure in- cludes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStru…