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1

An exaple of template based protein structure modeling by global optimization

Joo K., Joung I., Lee J.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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2016

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Vol. 20, No 4

341--352

EN

CASP (Critical Assessment of protein Structure Prediction) is a community-wide experiment for protein structure prediction taking place every two years since 1994. In CASP 11 held in 2014, according to the official CASP 11 assessment, our method named `nns' was ranked as the second best server method based on models ranked as first out of 81 targets. In `nns', we applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For the fold recognition, a new alignment method called CRF align was used. The good performance of the nns server method is attributed to the successful fold recognition carried out by combined methods including CRF align, and the current modeling formulation incorporating accurate structural aspects collected from multiple templates. In this article, we provide a successful example of `nns' predictions for T0776, for which all details of intermediate modeling data are provided.

2

G-DNA – a highly efficient multi-GPU/MPI tool for aligning nucleotide reads

Frohmberg W., Kierzynka M., Blazewicz J., Gawron P., Wojciechowski P.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2013

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Vol. 61, nr 4

989--992

EN

DNA/RNA sequencing has recently become a primary way researchers generate biological data for further analysis. Assembling algorithms are an integral part of this process. However, some of them require pairwise alignment to be applied to a great deal of reads. Although several efficient alignment tools have been released over the past few years, including those taking advantage of GPUs (Graphics Processing Units), none of them directly targets high-throughput sequencing data. As a result, a need arose to create software that could handle such data as effectively as possible. G-DNA (GPU-based DNA aligner) is the first highly parallel solution that has been optimized to process nucleotide reads (DNA/RNA) from modern sequencing machines. Results show that the software reaches up to 89 GCUPS (Giga Cell Updates Per Second) on a single GPU and as a result it is the fastest tool in its class. Moreover, it scales up well on multiple GPUs systems, including MPI-based computational clusters, where its performance is counted in TCUPS (Tera CUPS).

3

Efficient alternatives to PSI-BLAST

Startek M., Lasota S., Sykulski M., Bułak A., Noé L., Kucherov G., Gambin A.

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2012

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Vol. 60, nr 3

495-505

EN

In this paper we present two algorithms that may serve as efficient alternatives to the well-known PSI BLAST tool: SeedBLAST and CTX-PSI Blast. Both may benefit from the knowledge about amino acid composition specific to a given protein family: SeedBLAST uses the advisedly designed seed, while CTX-PSI BLAST extends PSI BLAST with the context-specific substitution model. The seeding technique became central in the theory of sequence alignment. There are several efficient tools applying seeds to DNA homology search, but not to protein homology search. In this paper we fill this gap. We advocate the use of multiple subset seeds derived from a hierarchical tree of amino acid residues. Our method computes, by an evolutionary algorithm, seeds that are specifically designed for a given protein family. The seeds are represented by deterministic finite automata (DFAs) and built into the NCBI-BLAST software. This extended tool, named SeedBLAST, is compared to the original BLAST and PSI-BLAST on several protein families. Our results demonstrate a superiority of SeedBLAST in terms of efficiency, especially in the case of twilight zone hits. The contextual substitution model has been proven to increase sensitivity of protein alignment. In this paper we perform a next step in the contextual alignment program. We announce a contextual version of the PSI-BLAST algorithm, an iterative version of the NCBI-BLAST tool. The experimental evaluation has been performed demonstrating a significantly higher sensitivity compared to the ordinary PSI-BLAST algorithm.

4

Application of bioinformatics methods to recognition of network threats

Kozakiewicz A., Felkner A., Kijowski P., Kruk T. J.

Journal of Telecommunications and Information Technology

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2007

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nr 4

23-27

EN

Bioinformatics is a large group of methods used in biology, mostly for analysis of gene sequences. The algorithms developed for this task have recently found a new application in network threat detection. This paper is an introduction to this area of research, presenting a survey of bioinformatics methods applied to this task, outlining the individual tasks and methods used to solve them. It is argued that the early conclusion that such methods are ineffective against polymorphic attacks is in fact too pessimistic.