Authors: Hota MK, Srivastava VK
In this paper, the performance of various sliding window trigonometric fast transforms for identification of protein coding regions has been analysed at the nucleotide level. It is found that, Short-Time Discrete Fourier Transform (ST-DFT) gives better identification accuracy in comparison with Short-Time Discrete Cosine Transform (ST-DCT), Short-Time Discrete Sine Transform (ST-DST) and Short-Time Discrete Hartley Transform (ST-DHT). In the proposed method, identification accuracy of protein coding regions has been improved by applying Singular Value Decomposition (SVD) on the DNA spectrum obtained using sliding window trigonometric fast transforms. The results show that, in proposed method all trigonometric fast transforms gives almost similar results …

We describe a novel approach to predict the structure of key TR features and to aid the identification of TRs in genomes, using a program we developed, TRFolder. We applied our method to confirm and improve previously studied core structures from Saccharomyces and Kluyveromyces TRs. We made novel structural predictions of core elements of the TRs from Schizosaccharomyces pombe, Candida albicans, and several other yeast species.
PMID: 21441097 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)

Authors: Jean G, Nikolski M
Current methods for detecting synteny work well for genomes with high degrees of inter- and intra-species chromosomal homology, such as mammals. This paper presents a new algorithm for synteny computation that is well suited to genomes covering a large evolutionary span. It is based on a three-step process: identification of initial microsyntenic homologous regions, extension of homologous boundaries and reconstruction of syntenic blocks by identification of groups of homologous genomic segments that are conserved in every subject genome. Our method performs as well as GRIMM-Synteny on mammalian genomes, and outperforms it for clades with much greater evolutionary distances such as the Hemiascomycetous yeasts.
PMID: 21441096 [PubMed - in process] (Source…

Authors: Chiu SK, Hsieh MH, Tzeng CM
By taking advantage of the power of comparative genomics, we devised an algorithm, Unique Marker Finder (U-MarFin), to generate a collection of unique DNA sequences from a target organism. The whole target genome is partitioned into a scoring pool of less 4000 base-pair fragments, which are then subjected to elimination of homologous sequences in other bacterial genomes by BLAST alignment, and looked for all open reading frames as they may be applied as unique markers. Through regular, nested, multiplex and real time PCR and microarray technology, we empirically demonstrated that the sequences discovered were highly specific to the species that they are derived from, and they can serve as molecular biomarkers for diagnostic purpose.
PMID: 214410…

This study is useful in making more accurate prediction of results with better combination Highly Active Antiretroviral Therapy (HAART) and important mutations.
PMID: 21441094 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)

This study sets out to check similar pattern, domain and residue-specific mutation, which may interact with expressions of P53 and BRCA1.
PMID: 21441093 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)

AbstractSome fungi cause disease in humans and plants, while others have demonstrable potential for the control of insect pests. In addition, fungi are also a rich reservoir of therapeutic metabolites and industrially‐useful enzymes. Detailed analysis of fungal biochemistry is now enabled by multiple technologies including protein mass spectrometry, genome and transcriptome sequencing and advances in bioinformatics. Yet, the assignment of function to fungal proteins, encoded either by in silico annotated, or unannotated genes, remains problematic. The purpose of this review is to describe the strategies used by many researchers to reveal protein function in fungi, and more importantly, to consolidate the nomenclature of ‘unknown function protein’, or UFP, as opposed to ‘hypothetica…

Conclusions: Our results show miR-663 may play an important role in ATRA induced HL-60 cell differentiation. Lentivirus delivery of miR-663 could potentially be used directly as an anticancer treatment in hematological malignancies. (Source: Journal of Hematology and Oncology)

We describe a new method to generate a smooth algebraic spline (AS) approximation of the molecular surface (MS) based on an initial coarse linear triangulation derived from the atomic coordinate information of biomolecules, present in the PDB (Protein Data Bank). Our method first constructs a triangular prism scaffold covering the MS triangulation, and then generates a piecewise polynomial function F in the Bernstein-Bezier (BB) basis within the scaffold. An ASMS (algebraic spline molecular surface) of the molecular surface is extracted as the zero contours of F which is almost C 1 everywhere, and has dual implicit and parametric representations. The dual representations allow us to easily construct Gaussian quadrature point and normal samplings of the ASMS and apply it to the accurate est…

Authors: Uehara H, Iwasaki Y, Wada C, Ikemura T, Abe T
Although remarkable progress in metagenomic sequencing of various environmental samples has been made, large numbers of fragment sequences have been registered in the international DNA databanks, primarily without information on gene function and phylotype, and thus with limited usefulness. Industrial useful biological activity is often carried out by a set of genes, such as those constituting an operon. In this connection, metagenomic approaches have a weakness because sets of the genes are usually split up, since the sequences obtained by metagenome analyses are fragmented into 1-kb or much shorter segments. Therefore, even when a set of genes responsible for an industrially useful function is found in one metagenome library, it …