Baker-Akhiezer Modules on Rational Varieties

The free Baker-Akhiezer modules on rational varieties obtained from ${\mathbb C}P^{1}\times{\mathbb C}P^{n-1}$ by identification of two hypersurfaces are constructed. The corollary of this construction is the existence of embedding of meromorphic function ring with some fixed pole into the ring of matrix differential operators in $n$ variables

PHOG-BLAST – a new generation tool for fast similarity search of protein families

BACKGROUND: The need to compare protein profiles frequently arises in various protein research areas: comparison of protein families, domain searches, resolution of orthology and paralogy. The existing fast algorithms can only compare a protein sequence with a protein sequence and a profile with a sequence. Algorithms to compare profiles use dynamic programming and complex scoring functions. RESULTS: We developed a new algorithm called PHOG-BLAST for fast similarity search of profiles. This algorithm uses profile discretization to convert a profile to a finite alphabet and utilizes hashing for fast search. To determine the optimal alphabet, we analyzed columns in reliable multiple alignments and obtained column clusters in the 20-dimensional profile space by applying a special clustering procedure. We show that the clustering procedure works best if its parameters are chosen so that 20 profile clusters are obtained which can be interpreted as ancestral amino acid residues. With these clusters, only less than 2% of columns in multiple alignments are out of clusters. We tested the performance of PHOG-BLAST vs. PSI-BLAST on three well-known databases of multiple alignments: COG, PFAM and BALIBASE. On the COG database both algorithms showed the same performance, on PFAM and BALIBASE PHOG-BLAST was much superior to PSI-BLAST. PHOG-BLAST required 10–20 times less computer memory and computation time than PSI-BLAST. CONCLUSION: Since PHOG-BLAST can compare multiple alignments of protein families, it can be used in different areas of comparative proteomics and protein evolution. For example, PHOG-BLAST helped to build the PHOG database of phylogenetic orthologous groups. An essential step in building this database was comparing protein complements of different species and orthologous groups of different taxons on a personal computer in reasonable time. When it is applied to detect weak similarity between protein families, PHOG-BLAST is less precise than rigorous profile-profile comparison method, though it runs much faster and can be used as a hit pre-selecting tool

Rodent-specific alternative exons are more frequent in rapidly evolving genes and in paralogs

<p>Abstract</p> <p>Background</p> <p>Alternative splicing is an important mechanism for generating functional and evolutionary diversity of proteins in eukaryotes. Here, we studied the frequency and functionality of recently gained, rodent-specific alternative exons.</p> <p>Results</p> <p>We projected the data about alternative splicing of mouse genes to the rat, human, and dog genomes, and identified exons conserved in the rat genome, but missing in more distant genomes. We estimated the frequency of rodent-specific exons while controlling for possible residual conservation of spurious exons. The frequency of rodent-specific exons is higher among predominantly skipped exons and exons disrupting the reading frame. Separation of all genes by the rate of sequence evolution and by gene families has demonstrated that rodent-specific cassette exons are more frequent in rapidly evolving genes and in rodent-specific paralogs.</p> <p>Conclusion</p> <p>Thus we demonstrated that recently gained exons tend to occur in fast-evolving genes, and their inclusion rate tends to be lower than that of older exons. This agrees with the theory that gain of alternative exons is one of the major mechanisms of gene evolution.</p

PHOG: a database of supergenomes built from proteome complements

BACKGROUND: Orthologs and paralogs are widely used terms in modern comparative genomics. Existing procedures for resolving orthologous/paralogous relationships are often based on manual revision of clusters of orthologous groups and/or lack any rigorous evolutionary base. DESCRIPTION: We developed a completely automated procedure that creates clusters of orthologous groups at each node of the taxonomy tree (PHOGs – Phylogenetic Orthologous Groups). As a result of this procedure, a tree of orthologous groups was obtained. Each cluster is a "supergene" and it is represented by an "ancestral" sequence obtained from the multiple alignment of orthologous and paralogous genes. The procedure has been applied to the taxonomy tree of organisms from all three domains of life. Protein complements from 50 bacterial, archaeal and eukaryotic species were used to create PHOGs at all tree nodes. 51367 PHOGs were obtained at the root node. CONCLUSION: The PHOG database demonstrates that it is possible to automatically process any number of sequenced genomes and to reconstruct orthologous and paralogous relationships between genomes using a rigorous evolutionary approach. This database can become a very useful tool in various areas of comparative genomics

Positron annihilation spectroscopy of vacancy-type defects hierarchy in submicrocrystalline nickel during annealing

Positron annihilation and X-ray diffraction analysis have been used to study submicrocrystalline nickel samples prepared by equal channel angular pressing. In the as-prepared samples the positrons are trapped at dislocation-type defects and in vacancy clusters that can include up to 5 vacancies. The study has revealed that the main positron trap centers at the annealing temperature of deltaT= 20°C-180°C are low-angle boundaries enriched by impurities. At deltaT = 180°C-360°C, the trap centers are low-angle boundaries providing the grain growth due to recrystallization in-situ

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

<p>Abstract</p> <p>Background</p> <p>Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.</p> <p>Results</p> <p>We present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server <url>http://bioinf.fbb.msu.ru/SDPfoxWeb/</url> and a stand-alone Java application available from the website.</p> <p>Conclusions</p> <p>SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.</p