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Integrating dbSNP with P. falciparum genome resources

Integrating dbSNP with P. falciparum genome resources. External mutation databases. Submitted SNP (ss4563). Reference SNP Record (rs228). Submitted SNP (ss770). Submitted SNP (ss228). Linkout. NCBI linked resources LocusLink, PubMed, GenBank, dbSTS

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Integrating dbSNP with P. falciparum genome resources

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  1. Integrating dbSNP with P. falciparum genome resources

  2. External mutation databases Submitted SNP (ss4563) ReferenceSNPRecord (rs228) Submitted SNP (ss770) Submitted SNP (ss228) Linkout • NCBI linked resources • LocusLink, PubMed, GenBank, dbSTS • Genome sequence (contig assemblies) • Map Viewer Linkout Summary validation information Summary variation information

  3. Queries within dbSNP: By organism: [ORGN] = “*falciparum*” returns: all variations for P. falciparum

  4. Queries within dbSNP: By strain: [STRAIN] = “K1” returns: all variations ascertained in samples that include strain K1

  5. Queries within dbSNP: By keyword: [COMMENT] = “*sulphadoxine*” By keyword: [COMMENT] = “*resistance*” returns: all variations with word

  6. dbSNP Haplotype Report HAP: DHPS-K1 ORGN: Plasmodium falciparum MAP: chr 8 GENE: Dihydropteroate synthetase COMMENT: possible resistance to sulphadoxine DEFINITION: ss# rs# Allele 869709 470124 C 869710 470125 G 869711 470126 C 869712 470127 T dbSNP Haplotype Report HAP: DHHS-K1 ORGN: Plasmodium falciparum MAP: chr 9 GENE: falcipain 2 DEFINITION: ss# rs# Allele 871701 544124 A 871702 544125 C 871703 544126 T 871701 871702 871703 The query [STRAIN]=“K1” returned 2 haplotypes. DHPS-K1 DHHS-K1 Haplotypes within dbSNP:

  7. Queries from Entrez Nucleotide via LINKOUT:

  8. Queries from Entrez PubMed via LINKOUT:

  9. Results of Integration Process: • Catalog of variations in dbSNP • Future annotation of variants on reference sequences • Query by keywords, gene name, strain within dbSNP • Query by Accession/Publication within Entrez • Query by nucleotide sequence via dbSNP blast service • Future query by map location via map view

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