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Biological Research

Print version ISSN 0716-9760

Abstract

ALI, Shabana Kouser; GEORGE PRIYA DOSS, C; THIRUMAL KUMAR, D  and  ZHU, Hailong. CoagVDb: a comprehensive database for coagulation factors and their associated SAPs. Biol. Res. [online]. 2015, vol.48, pp.1-8. ISSN 0716-9760.  http://dx.doi.org/10.1186S/40659-015-0028-5.

The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exert their effects, and ultimately interrogating this information for association with complex phenotypes. This work focuses on coagulation factors involved in the coagulation cascade pathway which plays a vital role in the maintenance of homeostasis in the human system. We developed an integrated coagulation variation database, CoagVDb, which makes use of the biological information from various public databases such as NCBI, OMIM, UniProt, PDB and SAPs (rsIDs/variant). CoagVDb enriched with computational prediction scores classify SAPs as either deleterious or tolerated. Also, various other properties are incorporated such as amino acid composition, secondary structure elements, solvent accessibility, ordered/disordered regions, conservation, and the presence of disulfide bonds. This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information. We hope our database will act as a useful reference resource for hematologists to reveal protein structure-function relationship and disease genotype-phenotype correlation.

Keywords : Coagulation cascade pathway; Coagulation factor proteins; Single amino acid substitutions; SIFT; PolyPhen 2; I-Mutant 3; Fathmm; Align GVGD; PhD-SNP; SNPs& GO; SNAP.

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