※ Computational resources of protein phosphorylation:
<2> Computational Tools
Last updated: June 8, 2009
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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.
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).
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).
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).
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.
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).
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.
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).
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.
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).