GAME: a simple and efficient whole genome alignment method using maximal exact match filtering

In this paper, we present a simple and efficient whole genome alignment method using maximal exact match (MEM). The major problem with the use of MEM anchor is that the number of hits in non-homologous regions increases exponentially when shorter MEM anchors are used to detect more homologous regions. To deal with this problem, we have developed a fast and accurate anchor filtering scheme based on simple match extension with minimum percent identity and extension length criteria. Due to its simplicity and accuracy, all MEM anchors in a pair of genomes can be exhaustively tested and filtered. In addition, by incorporating the translation technique, the alignment quality and speed of our genome alignment algorithm have been further improved. As a result, our genome alignment algorithm, GAME (Genome Alignment by Match Extension), performs competitively over existing algorithms and can align large whole genomes, e.g., A. thaliana, without the requirement of typical large memory and parallel processors. This is shown using an experiment which compares the performance of BLAST, BLASTZ, PatternHunter, MUMmer and our algorithm in aligning all 45 pairs of 10 microbial genomes. The scalability of our algorithm is shown in another experiment where all pairs of five chromosomes in A. thaliana were compared.     

Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the alpha carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail.     

Visible light induced tandem reactions: An efficient one pot strategy for constructing quinazolinones using in-situ formed aldehydes under photocatalyst-free and room-temperature conditions

A facile tandem route has been developed for constructing quinazolinones from various aminobenzamides and in-situ generated aldehydes. Visible light was found to play a dual role: first oxidizes the alcohol to the aldehyde and then facilitates its cyclization with o-substituted aniline. Furthermore, alcohols are perfect alternatives to aldehydes because they are greener, more available, more economical, more stable, and less toxic than aldehydes. The first reaction step continuously provides material for the second step, which effectively reduces loss through volatilization, oxidation, and polymerization of the aldehyde, while avoiding its toxicity. A variety of quinazolinones can be prepared in the presence of visible light without any additional photocatalyst. The developed synthesis protocol proceeds with the merits of mild conditions, broad substrate scope, operational simplicity, and high atom efficiency, with an eco-energy source under metal-free, photocatalyst-free, and ambient conditions.     

Phenanthroline-fluorescein molecular hybrid as a ratiometric and selective fluorescent chemosensor for Cu2+ via FRET strategy: synthesis,computational studies and in vitro applications

A FRET-based chemosensor L containing donor phenanthroline and acceptor fluorescein moiety was designed, synthesised and characterised for the ratiometric fluorescent detection of Cu²⁺ in organo-aqueous solution. Probe L showed high selectivity and excellent sensitivity towards Cu²⁺ ions by exhibiting both colorimetric and fluorometric changes due to opening of the spirolactum ring of fluorescein upon complexation with Cu²⁺. In presence of Cu²⁺ ions, probe L formed L-Cu²⁺ complex in 1:1 stoichiometric fashion which is established on the basis of Job’s plot and mass spectroscopy. We also performed DFT computational studies to know the binding nature and coordination feature of the complex. Furthermore, fluorescence imaging studies revealed that probe L was cell permeable and could be used to detect intracellular Cu²⁺ in living cells.