Systems for re-annotations of DNA microarray data for supporting analysis of results of DNA microarray experiments are becoming important elements of bioinformatics aspects of gene expression based studies [10]. However, due to the computational problems related to the whole genome browsing projects, available services and data for reannotation of microarray probes are still quite sparse. The d...

Up-regulation of human endogenous retroviruses (HERVs) is associated with many diseases, including cancer. In this study, an H family HERV (HERV-H)-related gene was identified and characterized. Its spliced transcript lacks protein-coding capacity and may belong to the emerging class of noncoding RNAs (ncRNAs). The 1.3-kb RNA consisting of four exons is transcribed from an Alu element upstream ...

We describe YASS – a new tool for finding local similarities in DNA sequences. The YASS algorithm first scans the sequence(s) and creates on the fly groups of seeds (small exact repeats obtained by hashing) according to statistically-founded criteria. Then it tries to extend those groups into similarity regions on the basis of a new extension criterion. The method can be seen as a compromise be...

BACKGROUND A large number of sensitive homology searches are required for mapping DNA sequence fragments to known protein sequences in public and private databases during metagenomic analysis. BLAST is currently used for this purpose, but its calculation speed is insufficient, especially for analyzing the large quantities of sequence data obtained from a next-generation sequencer. However, fast...

Gallus GBrowse (http://birdbase.net/cgi-bin/gbrowse/gallus/) provides online access to genomic and other information about the chicken, Gallus gallus. The information provided by this resource includes predicted genes and Gene Ontology (GO) terms, links to Gallus In Situ Hybridization Analysis (GEISHA), Unigene and Reactome, the genomic positions of chicken genetic markers, SNPs and microarray ...

Mammalian ALDH3 genes (ALDH3A1, ALDH3A2, ALDH3B1 and ALDH3B2) encode enzymes of peroxidic and fatty aldehyde metabolism. ALDH3A1 also plays a major role in anterior eye tissue UV-filtration. BLAT and BLAST analyses were undertaken of several vertebrate genomes using rat, chicken and zebrafish ALDH3-like amino acid sequences. Predicted vertebrate ALDH3 sequences and structures were highly conser...

With the completion of the rice genome sequencing, a standardized annotation is necessary so that the information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and manually curating all the genes in the rice genome. Here we present the Rice Annotation Project Databas...

MOTIVATION New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel' sequences in a complex dataset that are of interest and the superfluous sequences need to be removed. RESULTS A novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can a...