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Last Modified 2006-12-16
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SNP Search
: search SNPs by SNP name, e.g. snp.173.90.2994.I.2
Location : e.g. chr1:1-100 000, to search SNPs located in chromosome 1 from 1 bp to 100,000 bp.
Strand : forward/reverse
SNP Type : substitution/insertion/deletion
SNP in : SNPs detected in one of the three chicken strains of broiler/layer/Silkie
Quality Score in Reference : e.g. > = 97
Quality Score in Read : e.g. > = 50
SNPs in Gene : search SNPs on a given gene by gene name, e.g. riken1_5j5
SNPs in Reads : search SNPs on a given read by read name, e.g. rchsxb0_104909.y1.scf
Gene Search
Name : search genes/cDNAs by gene/cDNA tag according to different data sources.e.g. GGK123v (GenBank), riken1_27o15 (Riken1),ENST00000305123 (Ensembl).
Location : search genes located in a certain region of a chromosome.e.g. chr2:1-100 000, to search genes located in chromosome 2 from 1bp to 100,000 bp.
Ontology : search genes by Gene Ontology identifier, e.g. GO:0006808.
InterPro : search genes by InterPro identifier, e.g. IPR007275.
Keyword : search genes by functional description, e.g. "regulation of nitrogen utilization".
Sequence Search (SeqGetter)
SeqGetter allows extraction of variations residing within genomic domains. The sequence regions can be defined by chromosomal positions and types of genes or cDNAs. The output format can be chosen by the users.
Tracefile Search
Users may search graphics of raw sequence traces by tracefile name or tracefile-related SNPs.
QTL Search
Choose the chromosome and/or input the keyword for trait description, both full matching and fuzzy matching are available.
Reference Search
References with emphasis on chicken variation studies are collected and can be queried by Journal, Citation (Year, Volume, Page), Author and Title | Abstract | Full Text.

          MapView Help

MapView is a visualization tool that allows users to browse SNPs in genomic and functional context. MapView is composed of four types of sub-viewers in hierachical architecture, namely ChroView, GeneView, SNPView and TraceView. A factual report for each element contained in the visualization system is displayed automatically on demand.
ChroView:ChroView is based on the draft sequence of RJF. It contains basic information on the scale of chromosomes, such as length, distribution and statistics of genes/cDNAs and SNPs. Genomic sequences of the three domestic chickens (B: broiler, L: layer, S: Silkie) and QTLs are also aligned to the corresponding RJF chromosomal regions. ChroView allows users to center the map upon a point on the chromosome of interest and expand to obtain a more detailed view of genes/cDNAs, SNPs via GeneView and SNPView, respectively
GeneView:Present the zoom-in graphics for each specific gene/cDNA, such as exon-intron structures. ?Gene Report? is displayed automatically upon clicking.
SNPView:Present the zoom-in graphics for SNPs. SNPs in broiler, layer or Silkie are displayed by using different color schemes. ?SNP Report? is displayed automatically upon clicking.
TraceView: Graphical presentation of the original sequence traces around the detected SNP, Q-values for each nucleotide and the convenient position-location function further facilitate mutual interrogation and investigation of the SNPs.

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Supported by China National Grid Project   2002AA104250