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...yPhen-2 (5) single non-synonymous SNP No Yes No SIFT (6) a list of non-synonymous SNPs No Yes No SNPs3D (7) single non-synonymous SNP No Yes No PANTHER (8) single non-synonymous SNP No Yes No FASTSNP =-=(9)-=- a list of SNPs No Yes No F-SNP (10) single SNP No Yes No CandiSNPer (11) single SNP Yes Yes No SPOT (12) a list of SNPs, with or without P-values Yes Yes No GenomePipe of SNPinfo (13) a list of GWAS ...

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...regions affecting RNA splicing (ssSNPTarget) (12), miRNA target regions (PolymiRTS (13,14), Patrocles (15) and miRNASNP (16)), or multiple types of regulatory elements (FESD (17), F-SNP (18), FASTSNP =-=(19)-=- and SNP Function Portal (20)). These databases have supported functional SNP studies but did not introduce high-throughput experimentally identified regulatory elements into the functional analysis o...

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...wn to be detrimental as suggested by the high selection pressure on the splice sites among mammalian genomes (Burset et al., 2000). We note that other SNP prioritization studies (Bhatti et al., 2006; =-=Yuan et al., 2006-=-; Xu et al., 2005) assign the highest rank or score of functional impact to these two kinds of SNPs, as well. For the remaining cases, the confidence scores are obtained from the tools that are used t...

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...in dementia and ischemic stroke [19, 20]. Although there are presently several articles describing the association of SNPs in the IGF1R gene with different types of diseases, computational analysis has not yet been undertaken on the functional consequences of SNPs in this gene. We applied different publicly available computational algorithms, namely, Sorting Intolerant From Tolerant (SIFT) [21], Polymorphism Phenotyping (PolyPhen) [22], and Function Analysis and selection tool for single nucleotide polymorphisms (FASTSNP) to identify likely deleterious SNPs which could affect protein function [23]. The SIFT algorithm predicts whether an amino acid substitution affects protein function based on sequence homology among related genes and domains over evolutionary time, and the physical-chemical properties of the amino acid residues [24–26]. Sequence conservation and the nature of the amino acid residues involved are also incorporated by PolyPhen, but it also values the location of the substitution within known structures and structural features of the protein available in the annotated database SwissProt [5, 27]. By accessing a variety of heterogeneous biological databases and analytical ...

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... it is suggested that these findings are biological plausible. Using the software FASTSNP, rs16855458 and rs9288516 were predicted to cause changes of potential binding sites of transcription factors =-=(46)-=-, which may result in instability of XRCC5 messenger RNA transcript or dysfunction of XRCC5 expression, and finally in tumorigenesis. Additional work to characterize the functions of these two introni...

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...al (CI) 1.10-2.08; P=0.0133). FastSNP predicts thatsthis SNP is an intronic enhancer which may therefore be involved in affecting the stabilitysof the XRCC4 mRNA transcript or altering its expression =-=(38)-=-. Further analysis of this SNPsby Transfac (http://www.gene.regulation.com/index.htm) suggests that the presence of thesallele A instead of the G allele leads to loss of a GATA2 binding motif which ma...

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...onal annotations fromsvarious SNP-effect prediction tools along with other information such as minor allele frequency andsresidue conservationsTool URLsPolyDoms [30] http://polydoms.cchmc.orgsFASTSNP =-=[32]-=- http://fastsnp.ibms.sinica.edu.tw/sMutDB [33] http://mutdb.orgsF-SNP [34] http://compbio.cs.queensu.ca/F-SNP/s2.3 Current Features and Tools for Non-Coding PolymorphismsPrioritizationsAs discussed ea...