Current Bioinformatics - Volume 9, Issue 1, 2014

With the explosive growth of databanks consisting of protein sequences, there is an increasing need for annotating a number of newly discovered enzyme sequences. Given a protein sequence, the question arises on how to identify whether it is an enzyme or a non-enzyme? If it is an enzyme, and then which main functional class does it belong to? Since the biology experiment methods are both time-consuming and expensive, Read More

Research activities in the area of biological sciences, and particularly molecular microbiology, nowadays generate vast amounts of data. The development of faster and cheaper sequencing methods has definitively contributed to this huge amount of data, requiring the development of fast and reliable tools for their analysis. In the last years, many easy-to-use, reliable and powerful bioinformatics tools have been developed. Read More

Many bioinformatics analytical tools, especially for cancer classification and prediction, require complete sets of data matrix. Having missing values in gene expression studies significantly influences the interpretation of final data. However, to most analysts’ dismay, this has become a common problem and thus, relevant missing value imputation algorithms have to be developed and/or refined to address this matter. This paper i Read More

Ethnopharmacological findings are spread over several databases but are not well connected to other biomedical databases. Consequently, the utility of these sources as knowledge resources are limited. Herbal medicines have long been used for the treatment of different ailments and have attracted the attention of scientists and patients due to their easy availability, low cost, and affordability. Research is being performed on Read More

Meiotic recombination does not occur evenly across the genome, but instead occurs at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots). Recombination depends not only on sequence features, but also on chromatin structure. Identification and characterization of hotspots and coldspots are considerably significant as the information about hot/cold sp Read More

In this paper, an exhaustive algorithm for extracting structured motifs has been presented. Structured motif is defined as an ordered set of highly-conserved over-presented patterns which occur near each other in a set of DNA sequences .The presented algorithm is based on an innovative data structure called l-mer trie. As opposed to other existing motif finders, this algorithm offers more flexibility in terms of the possibility Read More

Fast development of new heuristic methods solving a multiple sequence alignment~(MSA) problem enforces a development of benchmarks for evaluation of the quality of these methods. One of the most reliable benchmarks relies on a comparison of an alignment created by a tested method and the reference alignment (which is usually created on the basis of some additional knowledge like its tertiary structure) store Read More

Production of high-quality crystals is one of the main bottlenecks in X-ray crystallography-based protein structure determination. In this paper we introduce PPCinter, a novel method to predict the propensity for production of diffraction-quality crystals, production of crystals, purification and production of protein material. PPCinter utilizes not only intra-molecular factors, but considers inter-molecular factors as well. Our meth Read More

Assessing and estimating essential parameters for a metabolic pathway by using a mathematical model is a significant step in Systems Biology. However, estimating process often faces numerous obstacles, for example when the number of unknown parameters escalates or data has noise, gets trapped in local minima and or having repeated exploration of poor solution during search process. Thus, this study proposes an im Read More

Prediction of coding region from genomic DNA sequence is the foremost step in the quest of gene identification. In the eukaryotic organism, the gene structure consists of promoter, intron, start codon, exon and stop codon, etc. In the prediction of splice site, which is the separation between exons and introns, the accuracy is lower than 90% even when the sequences adjacent to the splice sites have a high conservation. Ther Read More