Integrating dbSNP with Integrating dbSNP with P. falciparumP. falciparum genome genome
resourcesresources
Submitted SNP(ss228)
Submitted SNP(ss228)
Submitted SNP(ss770)
Submitted SNP(ss770)
External mutation
databases
External mutation
databases
LinkoutLinkout
NCBI linked resources LocusLink, PubMed, GenBank, dbSTS Genome sequence (contig assemblies) Map Viewer
NCBI linked resources LocusLink, PubMed, GenBank, dbSTS Genome sequence (contig assemblies) Map Viewer
Summary variation information
Summary variation information
Summary validation information
Summary validation information
ReferenceSNP
Record(rs228)
ReferenceSNP
Record(rs228)
LinkoutLinkout
Submitted SNP(ss4563)
Submitted SNP(ss4563)
¼CTTCTCTGTTACAAAA< >GAGATAAGCAAGTR¼CT
HumanSequence
All genomic sites potentially variable
dbSNPannotation
LocusLinkGenBank STS info
Genome Sequence
NCBI annotation:
Phenotypes and detailed loc us-specific knowledge:
Alleles
Levels of variation
Functional classification
Links to external databases
LinkOut
genomeproject
sequences
genomeproject
sequencesGenBanksequencerecords
GenBanksequencerecords
LocusLinkLocusLink
PubMedliteraturecitations
PubMedliteraturecitations
sequencetaggedsites
sequencetaggedsites
dbSNPdbSNP
The NCBI discovery space
LinkOutResourceIntegration
LinkOutResourceIntegration
TSC SNPconsortiumTSC SNP
consortium
NCI CGAPdatabase
NCI CGAPdatabase
locus-specificmutation db’slocus-specificmutation db’s
other centralvariation db’sother centralvariation db’s
Queries within dbSNP:Queries within dbSNP:
By organism: [ORGN] = “*falciparum*”By organism: [ORGN] = “*falciparum*”returns: all variations for P. falciparumreturns: all variations for P. falciparum
Queries within dbSNP:Queries within dbSNP:
By strain: [STRAIN] = “K1”By strain: [STRAIN] = “K1”returns: all variations ascertained in samples that include strain K1returns: all variations ascertained in samples that include strain K1
By keyword: [COMMENT] = “*sulphadoxine*”By keyword: [COMMENT] = “*sulphadoxine*”
returns: all variations with word returns: all variations with word
Queries within dbSNP:Queries within dbSNP:
By keyword: [COMMENT] = “*resistance*”By keyword: [COMMENT] = “*resistance*”
The query [STRAIN]=“K1”returned 2 haplotypes.DHPS-K1DHHS-K1
871701871702871703
dbSNP Haplotype Report
HAP: DHPS-K1ORGN: Plasmodium falciparumMAP: chr 8GENE: Dihydropteroate synthetaseCOMMENT: possible resistance to sulphadoxine
DEFINITION:ss# rs# Allele869709 470124 C869710 470125 G869711 470126 C869712 470127 T
Haplotypes within dbSNP:Haplotypes within dbSNP:
dbSNP Haplotype Report
HAP: DHHS-K1ORGN: Plasmodium falciparumMAP: chr 9GENE: falcipain 2
DEFINITION:ss# rs# Allele871701 544124 A871702 544125 C871703 544126 T
Queries from Entrez Nucleotide via LINKOUT:Queries from Entrez Nucleotide via LINKOUT:
Queries from Entrez PubMed via LINKOUT:Queries from Entrez PubMed via LINKOUT:
Results of Integration Process:Results of Integration Process:
• Catalog of variations in dbSNPCatalog of variations in dbSNP
• Future annotation of variants on reference sequencesFuture annotation of variants on reference sequences
• Query by keywords, gene name, strain within dbSNPQuery by keywords, gene name, strain within dbSNP
• Query by Accession/Publication within EntrezQuery by Accession/Publication within Entrez
• Query by nucleotide sequence via dbSNP blast serviceQuery by nucleotide sequence via dbSNP blast service
• Future query by map location via map viewFuture query by map location via map view