arXiv subjects

Simon Kogan

Publications and source records attributed to Simon Kogan.

3 recordsLinked to original sources

arXiv2013

Hierarchy of protein loop-lock structures: a new server for the decomposition of a protein structure into a set of closed loops

HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops - a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural "alphabet" of loops and locks.

physics.chem-ph↗

arXiv2004

Pattern overlapping decomposition by Cumulative Local Cross-Correlation

Background Nucleotide sequences contain multiple codes responsible for organism's functioning and structure. They can be investigated by various signal processing methods. These techniques are well suited for indication of frequently encountered sequence motifs (i.e., repeats). However, if there are two or more codes containing the same motif, the local nucleotide distribution (i.e., profile), resulting from sequence alignment by the motif position, will represent overlapping of the code patterns. Results The novel algorithm for decomposition of pattern overlapping is proposed. It is capable to work with dispersed repeats as well. The algorithm is based on cross-correlation procedure applied locally in a cumulative fashion. Its sensitivity was tested on human genomic sequences. Conclusions Cumulative Local Cross-Correlation was successfully used to decompose overlapping of nucleotide patterns in human genomic sequences. Being very general technique (as general as cross-correlation), it can be easily adopted in other signal processing applications and naturally extended for multidimensional cases. Software implementation of the algorithm is available on request from the authors.

q-bio.QM↗

arXiv2004

Gene splice sites correlate with nucleosome positions

Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential positioning of splice junctions within the nucleosomes. The RR and YY dinucleotides oscillate counterphase, i.e., their respective preferred positions are shifted about half-period one from another, as it was observed earlier for AA and TT dinucleotides. Species specificity of nucleosome positioning DNA pattern is indicated by predominant use of the periodical GG(CC) dinucleotides in human and mouse genes, as opposed to predominant AA(TT) dinucleotides in Arabidopsis and C.elegans. Keywords: chromatin; gene splicing; intron; exon; dinucleotide; periodical pattern

q-bio.GN↗