※ Computational resources of protein phosphorylation:


<1> Public Databases

<2> Computational Tools

<3> Others

Last updated: June 8, 2009


<1> Public Databases:

1. dbSNP: a database of single nucleotide polymorphisms. In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Cancer for Biotechnology Information (NCBI) has established the dbSNP database (Smigielski, et al., 2000).

2. HGMD: a comprehensive core collection of data on published germline mutations in nuclear genes underlying human inherited disease (Cooper, et al., 1998).

3. JSNP: a repository of Japanese Single Nucleotide Polymorphism (SNP) data,which serves as both a storage site for the Japanese SNPs and as a facility for public dissemination to allow researchers access to high quality SNP data (Hirakawa, et al., 2002).

4. ALFRED: the ALelle FREquency Database, a resource of gene frequency data on human populations supported by the U. S. National Science Foundation (Rajeevan, et al., 2003).

5. HGVbase: a curated resource describing human DNA variation and phenotype relationships (Fredman, et al., 2004).

6. UMD: a generic software which can be used to collect and analyze thousands of mutations are being identified in diagnostic and research laboratories (Béroud, et al., 2005).

7. SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions (Kim, et al., 2008).

8. AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants,the current version hosts data for the important crops rice, barley and Brassica (Duran, et al., 2009).

9. SNP2NMD: a database of human SNPs which result in PTCs (premature termination codons) and cause NMD (nonsense-mediated mRNA decay) (Han, et al., 2007).

10. SNP@Ethnos: a catalog of human SNPs and genes that contain human ethnic variation, the database contains some results for detecting natural selection and population difference (Park, et al., 2007).

11. FESD: a web-based integrated database for selecting sets of SNPs in putative functional elements such as promoter regions, CpG islands, 5'UTRs in human gene (Kang, et al., 2005).

12. dbSMR: a database of all miRNA binding sites within 200 nt of SNPs which may affect miRNA accessibility to the target site, thereby altering the regulation (Hariharan, et al., 2009).

13. SAAPdb: a new resource for the analysis and visualization of the structural effects of mutations. Its analytical approach is to map single nucleotide polymorphisms (SNPs) and pathogenic deviations (PDs) to protein structural data held within the Protein Data Bank (Hurst, et al., 2009).

14. Diseasome: an integrated database of genes, genetic variation, and diseases,provides a disease thesaurus with a tree view of that shows the number of genes that are associated with diseases, and a genome browser for conveniently looking up potentially deleterious SNPs among the genes that are strongly associated with specific diseases and clinical phenotypes (Yang, et al., 2008).

15. SNPper: a web-based application designed to facilitate the retrieval and use of human SNPs for high-throughput research purposes (Riva, et al., 2004).

16. CASCAD: a database designed for presentation and query of candidate SNPs that are retrieved by in silico mining of high-throughput sequencing data, Currently, the database provides collections of laboratory rat and zebrafish candidate SNPs (Guryev, et al., 2005).

17. YH: a server that allows the user to easily browse and download data from the first Asian diploid genome. the aim of this platform is to facilitate the study of this Asian genome and to enable improved organization and presentation large-scale personal genome data (Li, et al., 2009).

18. TcSNP: an online database with information on genetic variation (polymorphisms, mutations) for different stocks, strains and isolates of Trypanosoma cruzi, the causative agent of Chagas Disease (Ackermann, et al., 2009).

19. VarySysDB: a genetic polymorphism database based on 187,156 extensively annotated matured mRNA transcripts from 36,073 loci provided by H-InvDB. VarySysDB offers information encompassing published human genetic polymorphisms for each of these transcripts separately (Shimada, et al., 2009).

20. SPSmart: a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics (Amigo, et al., 2008).

21. FstSNP-HapMap3: a database of SNPs with High Population Differentiation for HapMap3, providing an enriched genotype dataset for approximately 1.6 million single nucleotide polymorphisms (SNPs) from 1,115 individuals with ancestry (Duan, et al., 2008).

22. SNP Function Portal: a web database for exploring the function implication of SNP alleles (Wang, et al., 2006).

23. JG-SNP: a common web resource to facilitate geriatric researches on the roles of genetic polymorphism (single nucleotide polymorphism, SNP) of Japanese (Sawabe, et al., 2004).

24. MonkeySNP: a web-based resource facilitating access to non-human primate (NHP) single nucleotide polymorphisms (SNP) data. It is a mirror of the NCBI dbSNP database and contains additional NHP subpopulation genotype data and visual genotype displays to support SNP review and selection (Khouangsathiene, et al., 2008).

25. topoSNP: The database provides an online resource for analyzing non-synonymous SNPs (nsSNPs) that can be mapped onto known 3D structures of proteins (Stitziel, et al., 2004).

26. StSNP: a webserver which compare structural nsSNP distributions in many proteins or protein complexes. StSNP enables researchers to map nsSNPs onto protein structures (Uzun, et al., 2007).

27. coliSNP: a database server that maps non-synonymous single nucleotide polymorphisms (nsSNPs) on the three-dimensional (3D) structure of proteins (Kono, et al., 2008).

28. FLYSNPdb: a database providing high-resolution single nucleotide polymorphism (SNP) data of Drosophila melanogaster (Chen, et al., 2009).

29. DigiPINS: a web-based tool for the selection of exonic SNPs obtained by in-silico analysis of EST data available in vertebrate genomes (Navratil, et al., 2008).

30. F-SNP: a collection of functional SNPs which provides integrated information about the functional effects of SNPs obtained from 16 bioinformatics tools and databases.The F-SNP database helps identify and focus on SNPs with potential pathological effect to human health (Lee, et al., 2008).

31. WASP: a web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations (Wangkumhang, et al., 2007). The database is not available.

32. V-MitoSNP: a web-based software platform that provides a user-friendly and interactive interface for mtSNP information, especially with regard to RFLP genotyping (Chuang, et al., 2006).

33. PIP: a web-based database platform providing detailed information of PIP(Potential Intron Polymorphism) markers and homologous relationships among PIP markers from different species (Yang, et al., 2007).

34. Mouse SNP Miner: a database of mouse SNPs predicted to cause missense, nonsense, frameshift, and splice-site mutations (Reuveni, et al., 2007).

35. DataBiNS: a Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein.The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway (Song, et al., 2007).

36. SNPSTR: a database of compound microsatellite-SNP markers, which combines a microsatellite marker (STR) with one or more tightly linked SNPs (Agrafioti, et al., 2007).

37. D-HaploDB: a web-accessible resource of genome-wide definitive haplotypes determined from a collection of Japanese complete hydatidiform moles (CHMs), each of which carries a genome derived from a single sperm (Higasa, et al., 2007).

38. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease, provides a means to derive a list of candidate SNPs to be evaluated in experimental or epidemiological studies for impact on protein functions and disease risk associations (Jegga, et al., 2007).

39. MamPol: a database of nucleotide polymorphism in the Mammalia class, containing all the well-annotated polymorphic sequences available in GenBank for the Mammalia class grouped by name of organism and gene (Egea, et al., 2007).

40. DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus, it allows the search for any polymorphic set according to different parameter values of nucleotide diversity, linkage disequilibrium and codon bias (Casillas, et al., 2005).

41. PolymiRTS: a collection of naturally occurring DNA variations in putative microRNA target sites, linking polymorphisms in microRNA target sites with complex traits (Bao, et al., 2007).

42. SNPeffect v2.0: a database useing sequence- and structure-based bioinformatics tools to predict the effect of non-synonymous SNPs on the molecular phenotype of proteins (Reumers, et al., 2006).

43. SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes (Packer, et al., 2006).

44. PICS: a database which classified and catalogued the predicted impact on protein function of non-synonymous single nucleotide polymorphisms (nsSNPs) in genes relevant to the biology of cancer using in silico computational tools (Rudd, et al., 2005).

45. dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods (Tahira, et al., 2005).

46. SAAP: a databse which integrate information on Single Amino Acid Polymorphisms (i.e. structurally expressed SNPs and mutations) with analysis of the likely structural effects of these amino acid mutations (Cavallo, et al., 2005).

47. ChickVD: a sequence variation database for the chicken genome,which contains 3.1 million non-redundant DNA sequence variants (Wang, et al., 2005).

48. IBISS: an interactive bovine in silico SNP (IBISS) database, which represents more than just a SNP database; it is also a genomic database containing uniformly annotated predicted gene mRNA and protein sequences, gene structure, and genomic organization information (Hawken, et al., 2004).

49. Indica/japonica SNPs: an SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments (Feltus, et al., 2004).

50. PromoLign: an online database application that presents SNPs and TF binding profiles in the context of human-mouse orthologous sequence alignment with a hyperlinked graphical interface (Zhao, et al., 2004).

51. VSD: a database established to systematically search for genes with small effect in the development of schizophrenia and to provide variation data for publicly available candidate genes (Zhou, et al., 2004). The database is not available.

52. PicSNP: a browsable catalog of nsSNPs(nonsynonymous single nucleotide polymorphisms) which are more likely to affect protein functions in the human genome (Chang, et al., 2001).

53. MutDB: a database annotating human variation with functionally relevant data and providing interactive mutation maps at the gene and protein levels (Mooney, et al., 2003).

54. rSNP_Guide: an integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites (Ponomarenko, et al., 2002).

55. SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data (Ponomarenko, et al., 2002).

56. SNPExpress: a database and its user interface that we developed to permit interrogation of the effects of common SNPs on exon and transcript level expression, in two different human tissues: brain and PBMC(Peripheral Blood Mononuclear Cell) (Sanders, et al., 2008).

57. PolyDoms: a database to integrate the results of multiple algorithmic procedures and functional criteria applied to the entire Entrez dbSNP dataset (Jegga, et al., 2007).

58. PhosphoVariant: a database for human genetic variations that influence proteins phosphorylation states (Ryu, et al., 2009).

<2> Computational toos:

1. Parepro: a method of identifying which non-synonymous single base changes have a deleterious effect on protein function, based on support vector machine (SVM) (Tian, et al., 2007).

2. PhD-SNP: a method based on support vector machines (SVMs) that starting from the protein sequence information can predict whether a new phenotype derived from a nsSNP can be related to a genetic disease in humans (Capriotti, et al., 2006).

3. PolyPhen: a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations (Ramensky, et al., 2002).

4. MAPP: a tool which predicts the impact of all possible amino acid substitutions on the function of the protein on the basis of this variation present in a column of a protein sequence alignment (Stone, et al., 2005).

5. SIFT: predicting whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations (Ng, et al., 2003).

6. SNPs3D: a website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis (Yue, et al., 2006).

7. LS-SNP: a genomic scale software which performs large-scale annotation of coding non-synonymous SNPs based on multiple information sources (Karchin, et al., 2005).

8. D2GSNP: is web-based tools for the selection of a set of SNPs within candidate genes of human diseases.

9. OpenADAM: an open source web-based data management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Affymetrix Genome-Wide Human SNP Array platforms (Yeung, et al., 2008).

10. Snap: a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome (Li, et al., 2007).

11. Gene Prospector: a bioinformatics tool designed to sort, rank, and display information about genes in relation to human diseases, risk factors and other phenotypes (Yu, et al., 2008).

12. SNP@WEB: a web-based catalog of SNP database and tools. Currently, SNP@WEB collected about 90 SNP resources classified into eight categories (SNP acquisition, annotation, tagSNP, haplotype, population, mutability, database, and SNP effect).

13. SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences.Users can investigate SNPs within protein domains with 2D and 3D maps (Han, et al., 2006).

14. HapMap filter 1.0: a tool to preprocess the HapMap genotypic data for association studies by specifying cell lines and two common filtering criteria: minor allele frequencies and genotyping rate (Zhang, et al., 2008).

15. SNPselector: a web tool for selecting SNPs for genetic association studies. It takes snp ID list, gene name list, or genome region list as input and searches SNPs for genome scan or gene assoctiation study (Xu, et al., 2005).

16. SNPsFinder: a web-based program developed to facilitate the SNPs discovery process. Complete genomic sequences or contig sequences of related organisms (strains and species) can be used for this analysis (Song, et al., 2005).

17. QuickSNP: a publicly accessible resource for the selection of variations (single nucleotide polymorphisms or SNPs) in the human genome than can be used for association studies in the context of genetic disorders (Grover, et al., 2007). The tool is not available.

18. TAMAL: an integrated approach to choosing SNPs in a specified set of candidate genes for genetic studies of human complex traits (Hemminger, et al., 2006).

19. Snagger: a program for incorporating additional information for tagSNP selection. It improves by providing a means to select tagSNPs that reliably capture genetic variation across multiple populations while accounting for significant genotyping failure risk and prioritizing on SNP-specific characteristics (Edlund, et al., 2008).

20. SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management, which allows for both ad hoc-mode and batch-mode SNP search, automatic SNP filtering, and retrieval of SNP data (Wang, et al., 2005).

21. ssSNPer: a novel user-friendly web interface identifying statistically similar SNPs to aid interpretation of genetic association studies (Nyholt, et al., 2006).

22. SNPLims: a data management system mainly devoted to the storage and management of SNP genotype data produced by the Illumina platform from the raw outputs of genotyping into a relational database (Orro, et al., 2008). The tool is not available.

23. MAVIANT: a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions (Panitz, et al., 2007).

24. PupasView: a visual tool for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level (Conde, et al., 2005).

25. PupaSNP Finder: a web tool for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect (Conde, et al., 2004). The tool is not available.

26. PupaSuite 2.0 : a web tool for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping projects (Conde, et al., 2006).

27. SNPP: a dynamic general database management system to manage high-throughput SNP genotyping data,It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting (Zhao, et al., 2005). The tool is not available.

28. easyLINKAGE-Plus: an extended version of the original easyLINKAGE program which added linkage analyses for large-scale SNP data in addition to those of microsatellites (Hoffmann, et al., 2005).

29. SNPLINK: a Perl script that performs full genome linkage analysis of high-density single nucleotide polymorphism (SNP) marker sets (Webb, et al., 2005).

30. ALOHOMORA: a tool for linkage analysis using 10K SNP array data, designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array (Rüschendorf, et al., 2005).

31. snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium(LD) plotting package (Luna, et al., 2007).

32. SNiPer: a new application which uses two clustering algorithms to yield increased call rates and equivalent concordance to Affymetrix called genotypes (Huentelman, et al., 2005).

33. SNiPer-HD: an improved SNP genotype calling program for highly accurate genotype calling across hundreds of thousands of SNPs (Hua, et al., 2007).

34. HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations (Gu, et al., 2005).

35. SNP-PHAGE: high throughput SNP discovery pipeline with additional features for identification of common haplotypes within a sequence tagged site (Haplotype Analysis) and GenBank (-dbSNP) submissions (Matukumalli, et al., 2006).

36. QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species (Tang, et al., 2006).

37. SNP-VISTA: an interactive SNP visualization tool for the analysis of large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles and massive amounts of ecogenomics data for studying homologous recombination in microbial populations (Shah, et al., 2005).

38. HaploSNPer: a flexible web-based tool for detecting SNPs and alleles in user-specified input sequences from both diploid and polyploid species (Tang, et al., 2008).

39. OSIRIS v1.2: a named entity recognition system used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases (Furlong, et al., 2008).

40. MutaGeneSys: a system that uses genome-wide SNP array data data to estimate individua disease susceptibility (Stoyanovich, et al., 2008).

41. FASTSNP: an always up-to-date web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects (Yuan, et al., 2006).

42. SNP Cutter: a web application which designs PCR-RFLP assays on a batch of SNPs from the human genome (Zhang, et al., 2005).

43. SNPbox: a modular software package that automates the design of PCR primers for large-scale amplification and sequencing projects in a standardized manner resulting in high quality PCR amplicons with a low failure rate (Weckx, et al., 2007).

44. SNP-RFLPing: a web-based software which provides the restriction enzyme for RFLP assays on a batch if SNPs and genes from the human, rat, and mouse genomes (Chang, et al., 2006).

45. SNP ID-info: a freeware to provide visualized SNP IDs within inputting genetic and physical information of genomes (Yang, et al., 2008).

46. SPR Opt: the first software to optimize the selection of forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input (Gardner, et al., 2005). The tool is not available.

47. SNPbrowser: a FREE tool enabling knowledge-guided selection of over six million TaqMan? or SNPlex System SNP Genotyping Assays, including 650 million genotypes generated for over three million SNPs validated by the International HapMap Project or Applied Biosystems in five major populations (De, et al., 2007).

48. PDA v.2: a web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups (Casillas, et al., 2006).

49. SNPmasker: a program to mask all SNPs in given sequence using information of dbSNP (Andreson, et al., 2006).

50. nsSNPCounter: a new tool that allows computation and analysis of synonymous and non-synonymous codon substitutions for studying evolutionary rates of protein coding genes (Khatri, et al., 2006).

51. ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants (Klaften, et al., 2005).

52. PolyMAPr: a program developed to improve the efficiency of database mining and polymorphism annotation ang functional analysis (Freimuth, et al., 2005). The tool is not available.

53. SNP Chart: a Java application for generating visual patterns that can be easily interpreted as a single specific Single Nucleotide Polymorphism (SNP) genotype, based on reiterative pattern recognition from validated SNP data (Tebbutt, et al., 2005).

54. SNPCEQer II: a GUI-based application that integrates single nucleotide polymorphism (SNP) detection, SNP analysis and SNP editing in the Microsoft Windows environment (Tang, et al., 2003).

55. blastNP: a novel sequence similarity searching and visualization method which is defined as a blastP that is performed on an overlappingly translated nucleic acid database using a similarly converted nucleic acid query (Biro, et al., 2004). (Not available)

56. GenotypeColour: a user-friendly tool able to upload, visualise and compare the huge amounts of data produced by Affymetrix Human Mapping GeneChips without losing the overall view of the data (Barlati, et al., 2009).

57. VarDetect: a stand-alone nucleotide variation exploratory tool that automatically detects nucleotide variation from fluorescence based chromatogram traces (Ngamphiw, et al., 2008).

58. InSNP: a windows program that detects substitution and indel SNPs in sequencing traces. It uses simple algorithms to detect the mutations and presents the sequences in compact visualizations that let you quickly decide which ones are real (Manaster, et al., 2005).

59. novoSNP: a software package which discovers single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (INDELs) in sequence trace files in a fast, reliable, and user-friendly way (Weckx, et al., 2005).

60. PolyScan: an algorithm and software implementation designed to provide de novo heterozygous indel detection and improved SNP identification in the context of high-throughput medical resequencing (Chen, et al., 2007).

61. SNPdetector: a software tool for automated identification of SNPs and mutations in fluorescence-based resequencing reads. It was designed to model the process of human visual inspection and has a very low false positive and false negative rate (Zhang, et al., 2005).

62. SeqDoC: a web-based tool to carry out direct comparison of ABI sequence chromatograms. It is ideal for small-scale SNP identification, for identification of changes in random mutagenesis screens, and for verification of PCR amplification fidelity (Crowe, et al., 2005).

63. SNPServer: a real-time flexible tool for the discovery of SNPs (single nucleotide polymorphisms) within DNA sequence data (Savage, et al., 2005). The tool is not available.

64. PolyPhred: a new computer program that automates the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing (Nickerson, et al., 1997).

65. FitSNPs: an effective tool to systematically prioritize candidate SNPs from genome-wide association studies based on the property that highly differentially expressed genes are more likely to have variants associated with disease (Chen, et al., 2008).

66. SNPMaP: a package which provides a framework for the analysis of SNP microarrays and pooling genome-wide association data using the tools available in the increasingly popular Open Source statistical computing environment (Davis, et al., 2009).

67. SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs (Beckstead, et al., 2008).

68. PrimerSNP: an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level, Experimental validation showed that this software had a successful prediction rate of 80.4 - 100% for strain specific primer design (Yao, et al., 2008).

69. SNPAnalyzer 2.0: a web-based SNP analysis tool embracing data quality check, linkage disequilibrium analysis and genetic association analysis in an integrated user interface (Yoo, et al., 2008).

70. SNPforID: a web-based tool for the query and visualization of the SNP allele frequency data generated by the SNPforID consortium (Amigo, et al., 2008).

71. Bovine SNP Retriever: a user-friendly tool for bovine SNP retrieval that also facilities the retrieval of SNP-related information within user-selected quantitative traits loci regions and reverse electronic polymerase chain reaction analysis on the bovine genome (Panzitta, et al., 2008).

72. SNPtoGO: a web-based tool which was developed to adds external information, i.e. GeneOntology (GO) terms to the analysis of SNP data (Schwarz, et al., 2008).

73. AffyMAPSDetector: a software tool to characterize Affymetrix GeneChip expression arrays with respect to SNPs, output from this tool characterizes SNP-containing probes on GeneChip microarrays (Kumari, et al., 2007).

74. CanPredict: a computational tool for predicting cancer-associated missense mutations, which will enable a large audience of biologists to determine which mutations are the most relevant for further study (Kaminker, et al., 2007).

75. SNPassoc: an R package to carry out most common analyses such as descriptive statistics and exploratory analysis of missing values, calculation of Hardy-Weinberg equilibrium, analysis of association based on generalized linear models and analysis of multiple SNPs in whole genome association studies (González, et al., 2007).

76. dChipSNP: an automated methods for making statistical significance analysis and clustering of SNP-array-based loss-of-heterozygosity data (Lin, et al., 2004).

77. SNPStats: a simple, ready-to-use software which has been designed to analyze genetic-epidemiology studies of association using SNPs (Solé, et al., 2006).

78. SNPchip: an R package which contains classes and methods useful for storing, visualizing and analyzing high density SNP array data (Scharpf, et al., 2007).

79. SNPscan: a web-accessible tool to analyze and visualize high density SNP data. It is useful to identify chromosomal abnormalities based on SNP intensity and heterozygosity data.SNPchip was inspired by the SNPscan webtool (Ting, et al., 2006).

80. SNPtrio: a web-based tool that allows visualization of uniparental inheritance segments based on single nucleotide polymorphism (SNP) genotype calls of father-mother-child trios (Ting, et al., 2007).

81. MegaSNPHunter: is the first approach that is capable of identifying the disease-associated SNP interactions from WTCCC studies and is promising for practical disease prognosis (Wan X, et al., 2009). This tool is not available.

82. SNPHarvester: a new method SNPHarvester to detect SNP-SNP interactions in GWA studies. SNPHarvester creates multiple paths in which the visited SNP groups tend to be statistically associated with diseases, and then harvests those significant SNP groups which pass the statistical tests (Yang C, et al., 2009).

<3> Others:

1. The SNP Consortium website & HapMap: The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. Data generated by the Project can be freely downloaded with minimal constraints (Thorisson, et al., 2003).

2. Variome: an openfree web resource which aims to support the international genome variance researches by collecting, organizing, analyzing, and disseminating difference among individuals and populations in one species (Han, et al., 2007).

3. The Human Variome Project: The Human Variome Project was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB) (Kaput, et al., 2009).