UNLABELLED Many existing databases annotate experimentally characterized single nucleotide polymorphisms (SNPs). Each non-synonymous SNP (nsSNP) changes one amino acid in the gene product (single amino acid substitution;SAAS). This change can either affect protein function or be neutral in that respect. Most polymorphisms lack experimental annotation of their functional impact. Here, we introdu...

Oculocutaneous albinism type II (OCA2) is the most common form of albinism in humans. OCA2 has been previously associated with mutations of the P gene, the human homologue to the murine pink-eyed dilution gene. The P gene encodes a 110 kDa protein containing 12 potential membrane spanning domains and is associated with melanosomal membranes. The specific function of the P protein is currently u...

Nucleotide sequence analyses of the Pvs48/45 and Pvs47 genes were conducted in 46 malaria patients from the Republic of Korea (ROK) (n = 40) and returning travellers from India (n = 3) and Indonesia (n = 3). The domain structures, which were based on cysteine residue position and secondary protein structure, were similar between Plasmodium vivax (Pvs48/45 and Pvs47) and Plasmodium falciparum (P...

X-linked adrenoleukodystrophy (X-ALD) is an inherited metabolic disease associated with mutations in the ABCD1 gene that encodes an ATP-binding cassette transporter protein, ALDP. The disease is characterized by increased concentrations of very long-chain fatty acids (VLCFAs) in plasma and in adrenal, testicular and nervous tissues, due to a defect in peroxisomal VLCFA β-oxidation. In the prese...

BACKGROUND Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged ov...

Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI) from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders an...

Title of Thesis: A web-based interactive visualization tool to explore patterns of amino acid substitution Kamalika Das, Master of Science, 2005 Thesis directed by: Dr. Penny Rheingans Among all the natural sciences, biology is the most data-rich subject. A few central databases of biology are growing exponentially in size with time. There has also been an exponential increase in the diversity ...

The adequacy of substitution matrices to model evolutionary relationships between amino acid sequences can be numerically evaluated by checking the mathematical property of triangle inequality for all triplets of residues. By converting substitution scores into distances, one can verify that a direct path between two amino acids is shorter than a path passing through a third amino acid in the a...

very little is known about lhr and fshr genes of domestic dromedary camels. the main objective of this study was to determine and analyze partial genomic regions of fshr and lhr genes in dromedary camels for the first time. to this end, a total of 50 dna samples belonging to dromedary camels raised in iran were sent for sequencing (25 samples of each gene). we compared the nucleotide sequences ...