We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are...

Gene function prediction is an important problem in bioinformatics. Due to the inherent noise existing in the gene expression data, the attempt to improve the prediction accuracy resorting to new classification techniques is limited. With the emergence of Gene Ontology (GO), extra knowledge about the gene products can be extracted from GO and facilitates solving the gene function prediction pro...

BACKGROUND Studies show that thousands of genes are associated with prognosis of breast cancer. Towards utilizing available genetic data, efforts have been made to predict outcomes using gene expression data, and a number of commercial products have been developed. These products have the following shortcomings: 1) They use the Cox model for prediction. However, the RSF model has been shown to ...

traditional poultry production has changed to a considerable industry after few decades. now, poultry industry is one of the main sectors to obtain the required protein for human consumption. prediction of the weight and number of eggs according to economic traits can improve the efficiency of production and the profit of producers. in present study, the weight and number of eggs in mazandaran ...

The accurate prediction of the translation start site, that is, the correct start codon, is important in order to analyze the putative protein product of a gene. Given the quality of the rest of the process, accurate start codon prediction is the most difficult remaining part of prokaryotic gene prediction. The gene-finding techniques discussed so far do little to predict the correct start codo...

Several works showed that biomolecular data integration is a key issue to improve the prediction of gene functions. Quite surprisingly only little attention has been devoted to data integration for gene function prediction through ensemble methods. In this work we show that relatively simple ensemble methods are competitive and in some cases are also able to outperform state-of-the-art data int...

Amelogenin gene (AMEL-X) encodes an enamel protein called amelogenin, which plays a vital role in tooth development. Any mutations in this gene or the associated pathway lead to developmental abnormalities of the tooth. The present study aims to analyze functional missense mutations in AMEL-X genes and derive an association with amelogenesis imperfecta. The information on miss...

We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished ...

The goal of gene finding is to locate genes, which are important segments of DNA encoding proteins. Programs solving this task are based on hidden Markov models (HMMs) capturing statistical features extracted from known genes, but often also incorporate hints about the correct gene structure extracted from experimental data. Existing gene finding programs can use such external information only ...

Gene finding, the accurate annotation of genomic DNA, has become one of the central topics in biological research. Although various computational methods (gene finders) have been proposed and developed, they all have their own limitations in gene findings. In this paper, we introduce an integrating gene finder, which combines the results of several existing gene finders together, to improve the...