FIND GENES, THEIR ASSOCIATED SEQUENCE READS, AND LESIONS DETECTED

Select Case(s) 454ests 454genomic Pc1GerminatingCysts Pc2GerminatingSporangia Pc3Zoospores Pc4EncystedZoospores Pc5FloodedMycelium Pc6DriedSporangia Pc7RichMedia Pc8PlitchMedia Pc9InfectedTomato SangerESTs SangerGenomic fl_cDNA infestans_genes kurt_est ramorum_genes sojae_genes Restrict by alignment type genomic transcriptomic both Results per page 50 100 200 500 1000 5000

Search by gene name starts with ends with exact match contains Restrict search to genes with associated read count >= and <= Restrict where at least reads call variant Restrict where at least uniquely aligned reads call variant Restrict where at least reads cover position Restrict where between % and % of reads call variant Restrict by associated variant type SNP    non-synonymous SNP    in/del    Restrict where variant in transcript coding region (CDS) Restrict where variant causes premature stop codon Restrict where in/del is not near a homopolymer

How To Search

Form is pre-populated with basic search criteria for identifying non-synonymous SNPs in pyrosequencing data. Click the "Clear" button to remove the pre-population; click "Reset" to return the form to the pre-populated state.

To select multiple cases, press "Ctrl" key while selecting case with left mouse button
To select all cases, press "Shift" key then select last case with left mouse button

The second column provides a series of filters and ways to restrict a search for genes and associated lesions. By entering values you increasingly restrict your search; but you can leave them empty also.

When searching by multiple candidate gene classes, candidate genes will be displayed regardless of which list they appear on.

The search can be restricted to query by variant type. Three options are available: SNP (Single Nucleotide Polymorphisms that do not cause an amino acid change), nsSNP (non-synonymous Single Nucleotide Polymorphisms within the coding region [CDS] that cause an amino acid change) and in/del (insertions or deletions).

The search can be restricted to in/dels that are not near a homopolymer. Near is defined as a window size of -6 to +4 positions from the in/del.