Computational problems of analysis of short next generation sequencing reads

Short read next generation sequencing (NGS) has significant impacts on modern genomics, genetics, cell biology and medicine, especially on meta-genomics, comparative genomics, polymorphism detection, mutation screening, transcriptome profiling, methylation profiling, chromatin remodelling and many more applications. However, NGS are prone for errors which complicate scientific conclusions. NGS technologies consist of shearing DNA molecules into collection of numerous small fragments, called a ‘library’, and their further extensive parallel sequencing. These sequenced overlapping fragments are called ‘reads’, they are assembled into contiguous strings. The contiguous sequences are in turn assembled into genomes for further analysis. Computational sequencing problems are those arising from numerical processing of sequenced samples. The numerical processing involves procedures such as: quality-scoring, mapping/assembling, and surprisingly, error-correction of a data. This paper is reviewing post-processing errors and computational methods to discern them. It also includes sequencing dictionary. We present here quality control of raw data, errors arising at the steps of alignment of sequencing reads to a reference genome and assembly. Finally this work presents identification of mutations (“Variant calling”) in sequencing data and its quality control

Computer analysis of co-localization of transcription factor binding sites in genome by ChIP-seq data

Statistical features of the distribution of transcription factor binding sites in the mouse genome that are obtained by ChIP-seq experiments in embryonic stem cells have been considered. Clusters of sites that contain four or more different transcription factor binding sites in the mouse genome have been defined, also their location relatively to the regulatory regions of genes has been described. The presence of two types of site co-localization has been shown: clusters containing binding sites for factors Oct4, Nanog, Sox2, located in the distal regions, and clusters containing binding sites n-Myc, c-Myc, mainly located in the promoter regions of mouse genes. Analysis of new ChIPseq data about binding of transcription factors Nr5a2, Tbx3 in the same cell type has confirmed the division of clusters of transcription factors binding sites into two types: those containing the binding sites of regulators of pluripotency (Oct4, Nanog, and others) and those not. The computer program of the statistical data processing of gene location and chromatin domains that analyzes experimental data of site localization obtained by ChIP-seq in the mouse genome and the human genome has been developed. The presence of preferences at position of transcription factor binding sites of various types has been revealed, the distances between the nearest groups of TF binding sites Oct4, Nanog, Sox2 and TF binding sites n-Myc and c-Myc have been calculated using this program. The presence of nucleotide motifs of transcription factor binding sites in the selected areas of ChIP-seq has been estimated, nucleotide motifs have been refined. A correlation between the presence of motifs and the intensity of ChIPseq binding has been shown. Computer methods for estimating the clustering of different transcription factors binding sites for new data ChIP-seq have been developed. Programs are available upon the request to the authors

[BETS]2\mathsf{_{2}}⋅C60\cdot{ C_{60 }} complex and BETS salts with square-planar platinate (II), nickelate (II) anions: (BETS)4{_{4}}⋅{\cdot} Pt(CN)4{_{4}}, (BETS)4{_{4}}⋅{\cdot} Ni(CN)4{_{4}}

The (BETS)$_{2}\cdot$C$_{60 }$ complex (1) and new radical cation salts based on bis(ethylenedithio)tetraselenafulvalene (BETS) with the square-planar [ Ni(CN)$_{4}$] $^{2-}$ , [ Pt(CN)$_{4}$] $^{2-}$ anions were synthesized: (BETS)$_{4}\cdot$Ni(CN)$_{4 }$(2), (BETS)$_{4}\cdot$Pt(CN)$_{4 }$(3). The crystal structure of 1 - 3 is layered. The layers consisting of C$_{60}$ molecules are alternated with the layers composed of BETS molecules in 1. The obtained complex is classified as molecular adduct in which the van der Waals interactions are predominant. The radical cation layers in the salt 2 are alternated with the anion layers along the ñ-direction of the unit cell. The salts retain metallic state down to 4.2 K. The band structure calculation of 2 shows 2-dimensional cylindrical Fermi surface, which is consistent with the $\theta$- type structure and its conductivity. Key words. Radical cation salts, bis(ethylenedithio)tetraselenafulvalene, tetracyanonickelate (II) anion, tetracyanoplatinate (II) anion, fullerene, crystal structure, electronic band structure calculation.