Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
SNPit: A federated data integration system for the purpose of functional SNP annotation
Computer Methods and Programs in Biomedicine
DILS'06 Proceedings of the Third international conference on Data Integration in the Life Sciences
Two birds, one stone: selecting functionally informative tag SNPs for disease association studies
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
International Journal of Bioinformatics Research and Applications
Hi-index | 3.84 |
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 to annotate nsSNPs. LS-SNP comprehensively maps nsSNPs onto protein sequences, functional pathways and comparative protein structure models, and predicts positions where nsSNPs destabilize proteins, interfere with the formation of domain--domain interfaces, have an effect on protein--ligand binding or severely impact human health. It currently annotates 28 043 validated SNPs that produce amino acid residue substitutions in human proteins from the SwissProt/TrEMBL database. Annotations can be viewed via a web interface either in the context of a genomic region or by selecting sets of SNPs, genes, proteins or pathways. These results are useful for identifying candidate functional SNPs within a gene, haplotype or pathway and in probing molecular mechanisms responsible for functional impacts of nsSNPs. Availability: http://www.salilab.org/LS-SNP Contact: rachelk@salilab.org Supplementary information: http://salilab.org/LS-SNP/supp-info.pdf