A package of fast tools for genomic sequence analysis

Here we present a current progress towards the develepment of nucleotide sequence analysis software package produced as a result of bioinformatics initiative at SFedU. Different modules included in the package allow to perform wide range of sophisticated operations including sequence alignment, motif search and de novo discovery, primer design etc. The particular advantage of the package modules is the reduced time of task performing coupled with optimization for memory usage both leading to improved performance. The latter was reached due to using special data structures, parallel running, etc. Widely used in bioinformatics pairwise alignments are represented by two pairwise alignment algorithms (parallel block and parallel block with optimal memory usage) adjusted to running on multi-core processors and accelerators. The performance tests have confirmed that the former one is faster than Needleman-Wunsch algorithm by ~60% and EMBOSS tool by This research was supported by project of the Ministry of Education and Science of Russia No6.703. 2014/K «The search of new targets for predictive diagnostics of the reproductive system diseases». Analytical work was carried out on the equipment of Center for collective use of Southern Federal University «High Technology», grant RFMEFI59414X0002. B. J. Steinberg is with the Southern Federal University, Institute of Mathematics, Mechanics and Computer Science, Rostov-on-Don, Russia (email: borsteinb@mail.ru). J. M. Abu-Khalil is with the Southern Federal University, Institute of Mathematics, Mechanics and Computer Science, Rostov-on-Don, Russia (email: jumana.abukhalil@gmail.com). M. G. Adigeyev is with the Southern Federal University, Institute of Mathematics, Mechanics and Computer Science, Rostov-on-Don, Russia (email: madi@math.sfedu.ru). A. A. Bout is with the Southern Federal University, Institute of Mathematics, Mechanics and Computer Science, Rostov-on-Don, Russia (email: a-bout@yandex.ru). A. V. Kermanov is with the Southern Federal University, Institute of Mathematics, Mechanics and Computer Science, and Research Institute for Plague Control, Rostov-on-Don, Russia (e-mail: av-kermanov@mail.ru). E. A. Pshenichnyy is with the Southern Federal University, Research Institute of Biology, Rostov-on-Don, Russia (e-mail: pshenichniy.eugene@gmail.com). G. V. Ramanchauskayte is with the Southern Federal University, Institute of Mathematics, Mechanics and Computer Science, Rostov-on-Don, Russia (e-mail: galinka@lastbit.com). A. P. Kroshkina is with the Southern Federal University, Institute of Mathematics, Mechanics and Computer Science, Rostov-on-Don, Russia (email: kroshkina.alena@yandex.ru). A. V. Gutnikov is with the Southern Federal University, Institute of Mathematics, Mechanics and Computer Science, Rostov-on-Don, Russia (email: zeratul477@gmail.com). N. S. Ponomareva is with the Southern Federal University, Institute of high technology and piezotechnique, Rostov-on-Don, Russia (e-mail: nsponomareva@sfedu.ru). A.E. Panich is with the Southern Federal University, Institute of high technology and piezotechnique, Rostov-on-Don, Russia (e-mail: panich@sfedu.ru). T. P. Shkurat is with the Southern Federal University, Research Institute of Biology, Rostov-on-Don, Russia (e-mail: tshkurat@sfedu.ru). ~30% . The latter one aligns long sequences faster than EMBOSS Stretcher by 40%. The motif discovery time was decreased tenfold for some conditions when Gibbs sampling method with truncated generalized suffix trees was introduced into algortihm. A VP-tree based approach offered for locating of genome origins of replications allowed to lower time complexity comparing with the naïve algorithm. Keywords— Bioinformatics, Dynamic programming, Suffix tree, Vp-tree.