Integrating dbSNP with P. falciparum genome resources.

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