Here we describe DataBiNS-Viz – a visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data gathered by the BioMoby-based DataBiNS workflow. DataBiNSViz enables execution of the DataBiNS workflow on proteins described by KEGG, PubMed, or OMIM identifiers, followed by manual exploration of the integrated structure/function and pathway data ...

Selectins are adhesion molecules, which mediate attachment between leucocytes and endothelium. They aid extravasation of leucocytes from blood into inflamed tissue during the mammary gland's response to infection. Selectins are also involved in attachment of the conceptus to the endometrium and subsequent placental development. Poor fertility and udder health are major causes for culling dairy ...

Neuropeptide S (NPS) has generated substantial interest due to its anxiolytic and fear-attenuating effects in rodents, while a corresponding receptor polymorphism associated with increased NPS receptor (NPSR1) surface expression and efficacy has been implicated in an increased risk of panic disorder in humans. To gain insight into this paradox, we examined the NPS system in rats and mice bred f...

Synonymous mutations are considered to be "silent" as they do not affect protein sequence. However, different silent codons have different translation efficiency (TE), which raises the question to what extent such mutations are really neutral. We perform the first genome-wide study of natural selection operating on TE in recent human evolution, surveying 13,798 synonymous single nucleotide poly...

BACKGROUND Mutations in SCN9A, encoding the alpha subunit of the voltage-gated sodium channel (Nav1.7), have caused severe pain disorders and congenital insensitivity to pain. The aim of this study was to validate the previously reported association between a common non-synonymous polymorphism (R1150W, rs6746030) in SCN9A and chronic widespread pain (CWP), in independent population-based cohort...

Clinical relevance is implicated between the genetic polymorphisms of the ABC (ATP-binding cassette) transporter ABCG2 (ABC subfamily G, member 2) and the individual differences in drug response. We expressed a total of seven non-synonymous SNP (single nucleotide polymorphism) variants in Flp-In-293 cells by using the Flp (flippase) recombinase system. Of these, ABCG2 F208S and S441N variants w...

MOTIVATION The NCBI dbSNP database lists over 9 million single nucleotide polymorphisms (SNPs) in the human genome, but currently contains limited annotation information. SNPs that result in amino acid residue changes (nsSNPs) are of critical importance in variation between individuals, including disease and drug sensitivity. RESULTS We have developed LS-SNP, a genomic scale software pipeline...

Abstract Background Stuttering is a fluency disorder typically characterized by part-word repetitions, voiced or voiceless sound prolongations, and broken words. Evidence suggests that 1% of the world population stutters. Compelling evidence from past research stuttering caused non-synonymous coding sites. This study evaluates intronic regions GNPTAB, GNPTG, NAGPA genes for possible pathogenici...

Next-generation sequencing allows the discovery of large numbers of single nucleotide polymorphisms (SNPs) in species where little genomic information was previously available. Here, we assembled, de novo, over 130 mb of non-normalized cDNA using 454 pyrosequencing data from dwarf and normal lake whitefish and backcross hybrids. Our main goals were to gather a large data set of SNP markers, doc...

In animals, the population genomic literature is dominated by two taxa, namely mammals and drosophilids, in which fully sequenced, well-annotated genomes have been available for years. Data from other metazoan phyla are scarce, probably because the vast majority of living species still lack a closely related reference genome. Here we achieve de novo, reference-free population genomic analysis f...