Index:
<1>
Public Databases
<2>
Computational Tools
<3>
Others
last updated: June 8, 2009
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<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 (B¨¦roud, 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£º
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 (R¨¹schendorf,
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£º
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 (Gonz¨¢lez,
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 (Sol¨¦,
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).
Last update: Aug. 10th, 2010