Secondary structure remains the most exploitable feature for noncoding RNA (ncRNA) gene finding in genomes. However, methods based on secondary structure prediction may generate superfluous amount of candidates for validation and have yet to deliver the desired performance that can complement experimental efforts in ncRNA gene finding. This paper investigates a novel method, unpaired structural...

MOTIVATION Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene fin...

Metagenomic sequencing projects yield numerous sequencing reads of a diverse range of uncultivated and mostly yet unknown microorganisms. In many cases, these sequencing reads cannot be assembled into longer contigs. Thus, gene prediction tools that were originally developed for whole-genome analysis are not suitable for processing metagenomes. Orphelia is a program for predicting genes in shor...

Metagenomics is an emerging field in which the power of genome analysis is applied to entire communities of microbes. It is focused on the understanding of the mixture of genes (genomes) in a community as whole. The gene prediction task is a well-known problem in genomics, and it remains an interesting computational challenge in metagenomics too. A large variety of classifiers has been develope...

The completion of the sequencing of the mouse genome promises to help predict human genes with greater accuracy. While current ab initio gene prediction programs are remarkably sensitive (i.e., they predict at least a fragment of most genes), their specificity is often low, predicting a large number of false-positive genes in the human genome. Sequence conservation at the protein level with the...

Here we provide the recent information on molecular profile of endometrium and highlight pathogenesis infertility occurring during endometriosis. Because individual features each woman’s organism, there are no versatile diagnostic criteria for determining endometrial receptivity which plays one leading roles in implantation disorders. Although a lot studies gene expression endometriosis have be...

BACKGROUND Today, despite the many advances in early detection of diseases, cancer patients have a poor prognosis and the survival rates in them are low. Recently, microarray technologies have been used for gathering thousands data about the gene expression level of cancer cells. These types of data are the main indicators in survival prediction of cancer. This study highlights the improvement ...

Evaluating large biological data sets requires perception of the data by inferring structure or generalizations from the data. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association...