EST-SNP database help page

Search settings

• SNP type includes C/T, A/G, transition, A/T, A/C, C/G, T/G, transversion, indel and all of these. required
• Advanced SNP type includes non-synonymous SNP or synonymous SNP in the matching protein region or coding region, as well as SNP's in the UTR region. The results are based upon protein database searching
• The reference species is the species providing the EST resource. required
• Search database by contig ID, SNP ID, the gbid for the EST, or a unigene ID. All contig ID's with SNP can be chosen by selecting "all contigs with SNP", such as 24. SNP id is contigid_snploci, such as "24_49". Gbid is Genbank ID of one EST. Unigene ID is from the unigene db.
• The D-value is used to screen clusters/contigs with paralogs. The D-value shows the discrepancy of the SNP number among haplotypes (paralogs or orthologs groups). A higher D-value indicated that the cluster/contig is likely to contain paralogs. Most of D-value is in the interval [0,1] in our study.

Output settings

• include alignment info shows alignment information of the contig and SNP location in the contig when searching by contig id

    For example:

• include summary info shows the statistical information about SNP of reference species
• include SNP blocks shows the blocks of SNP linked together in the contig. This works only when searching by contig id
• include SNP pattern shows all SNPs in the contig with same variation pattern. This works only when searching by contig id

• include EST annotator shows unigene, species and function information of all ESTs in the contig when searching by contig id
• include SNP for microarray shows SNP's that can be used for constructing probes for micro-array

• all contigs with SNP gives contig id, the number of EST, unigene id, and the number of true SNP's of all contigs with reliable SNP's
• ORF info of all contigs with SNP displays ORF information of all contigs with SNP