GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering

<div><p>Sequence homology searches are used in various fields and require large amounts of computation time, especially for metagenomic analysis, owing to the large number of queries and the database size. To accelerate computing analyses, graphics processing units (GPUs) are widely used as a low-cost, high-performance computing platform. Therefore, we mapped the time-consuming steps involved in GHOSTZ, which is a state-of-the-art homology search algorithm for protein sequences, onto a GPU and implemented it as GHOSTZ-GPU. In addition, we optimized memory access for GPU calculations and for communication between the CPU and GPU. As per results of the evaluation test involving metagenomic data, GHOSTZ-GPU with 12 CPU threads and 1 GPU was approximately 3.0- to 4.1-fold faster than GHOSTZ with 12 CPU threads. Moreover, GHOSTZ-GPU with 12 CPU threads and 3 GPUs was approximately 5.8- to 7.7-fold faster than GHOSTZ with 12 CPU threads.</p></div

Seed search algorithm using suffix arrays.

<p>Seed search algorithm using suffix arrays.</p

GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array

<div><p>DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity. However, huge amounts of sequence data create the problem that even general homology search analyses using BLASTX become difficult in terms of computational cost. We designed a new homology search algorithm that finds seed sequences based on the suffix arrays of a query and a database, and have implemented it as GHOSTX. GHOSTX achieved approximately 131–165 times acceleration over a BLASTX search at similar levels of sensitivity. GHOSTX is distributed under the BSD 2-clause license and is available for download at <a href="http://www.bi.cs.titech.ac.jp/ghostx/" target="_blank">http://www.bi.cs.titech.ac.jp/ghostx/</a>. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We offer this tool as a potential solution to this problem.</p></div

The flow of GHOSTX.

<p>The flow of GHOSTX.</p

Computation time with SRR444039 and NCBI nr (14.8 GB).

<p>The first, second, and third columns show the name of each program, the computation time, and the acceleration in processing speed relative to BLASTX using 1 thread, respectively.</p

Search for candidate alignments.

<p>Search for candidate alignments.</p

Calculation of an alignment in the region around a candidate position.

<p>Calculation of an alignment in the region around a candidate position.</p

MMS21/HPY2 and SIZ1, Two Arabidopsis SUMO E3 Ligases, Have Distinct Functions in Development

<div><p>The small ubiquitin related modifier (SUMO)-mediated posttranslational protein modification is widely conserved among eukaryotes. Similar to ubiquitination, SUMO modifications are attached to the substrate protein through three reaction steps by the E1, E2 and E3 enzymes. To date, multiple families of SUMO E3 ligases have been reported in yeast and animals, but only two types of E3 ligases have been identified in Arabidopsis: <u>S</u>AP and M<u>iz</u> 1 (SIZ1) and <u>M</u>ethyl <u>M</u>ethanesulfonate-<u>S</u>ensitivity protein <u>21</u> (MMS21)/<u>H</u>IGH <u>P</u>LOID<u>Y</u> 2 (HPY2), hereafter referred to as HPY2. Both proteins possess characteristic motifs termed <u>S</u>iz/<u>P</u>IAS RING (SP-RING) domains, and these motifs are conserved throughout the plant kingdom. Previous studies have shown that loss-of-function mutations in HPY2 or SIZ1 cause dwarf phenotypes and that the phenotype of <em>siz1-2</em> is caused by the accumulation of salicylic acid (SA). However, we demonstrate here that the phenotype of <em>hpy2-1</em> does not depend on SA accumulation. Consistently, the expression of <em>SIZ1</em> driven by the <em>HPY2</em> promoter does not complement the <em>hpy2-1</em> phenotypes, indicating that they are not functional homologs. Lastly, we show that the <em>siz1-2</em> and <em>hpy2-1</em> double mutant results in embryonic lethality, supporting the hypothesis that they have non-overlapping roles during embryogenesis. Together, these results suggest that SIZ1 and HPY2 function independently and that their combined SUMOylation is essential for plant development.</p> </div

Data flow and processing within GHOSTM.

<p>Data flow and processing within GHOSTM.</p

Search sensitivity of different search methods.

<p>Searches of ERR315856 sequences against the KEGG GENES database.</p