Effiicient Computation of Maximal Exact Matches Between Genomic Sequences

Sequence alignment is one of the most accomplished methods in the field of bioinformatics, being crucial to determine similarities between sequences, from finding genes to predicting functions. The computation of Maximal Exact Matches (MEM) plays a fundamental part in some algorithms for sequence alignment. MEMs between a reference-query genome are often utilized as seeds in a genome aligner to increase its efficiency. The MEM computation is a time consuming step in the sequence alignment process and increasing the performance of this step increases significantly the whole process of the alignment between the sequences. As of today, there are many programs available for MEM computing, from algorithms based full text indexes, like essaMEM; to more effective ones, such as E-MEM, copMEM and bfMEM. However, none of the available programs for the computation of MEMs are able to work with highly related sequences. In this study, we propose an improved version, E-MEM2, of the well known MEM computing software, E-MEM. With a trade-off between time and memory, the improved version shows to run faster than its previous version, presenting very large improvements when comparing closely-related sequences

Accurate and realistic initial data for black hole-neutron star binaries

This paper is devoted to the computation of compact binaries composed of one black hole and one neutron star. The objects are assumed to be on exact circular orbits. Standard 3+1 decomposition of Einstein equations is performed and the conformal flatness approximation is used. The obtained system of elliptic equations is solved by means of multi-domain spectral methods. Results are compared with previous work both in the high mass ratio limit and for one neutron star with very low compactness parameter. The accuracy of the present code is shown to be greater than with previous codes. Moreover, for the first time, some sequences containing one neutron star of realistic compactness are presented and discussed.Comment: Version including the erratum to be published in Phys. Rev.