Name : 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
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.
Users may search graphics of raw sequence traces by tracefile name or tracefile-related SNPs.
Choose the chromosome and/or input the keyword for trait description, both full matching and fuzzy matching are available.
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.