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Integrating dbSNP with P. falciparum genome resources.

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Presentation on theme: "Integrating dbSNP with P. falciparum genome resources."— Presentation transcript:

1 Integrating dbSNP with P. falciparum genome resources

2 Submitted SNP (ss228) Submitted SNP (ss228) Submitted SNP (ss770) Submitted SNP (ss770) External mutation databases Linkout 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 validation information Reference SNP Record (rs228) Reference SNP Record (rs228) Linkout Submitted SNP (ss4563) Submitted SNP (ss4563)

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

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

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

9 The query [STRAIN]=“K1” returned 2 haplotypes. DHPS-K1 DHHS-K dbSNP Haplotype Report HAP: DHPS-K1 ORGN: Plasmodium falciparum MAP: chr 8 GENE: Dihydropteroate synthetase COMMENT: possible resistance to sulphadoxine DEFINITION: ss# rs# Allele C G C T Haplotypes within dbSNP: dbSNP Haplotype Report HAP: DHHS-K1 ORGN: Plasmodium falciparum MAP: chr 9 GENE: falcipain 2 DEFINITION: ss# rs# Allele A C T

10 Queries from Entrez Nucleotide via LINKOUT:

11 Queries from Entrez PubMed via LINKOUT:

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


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