How do I use BLAST to obtain contig information?
- Clicking on the "BLAST contigs" button on the sub-menu will open a page where you can use homology searching (BLAST) to look for SNP containing contigs. Enter the DNA sequence into the main field and select the e-value cutoff that you require and start the BLAST search by clicking on the "Submit Query" button.
- This will produce a BLAST result page describing any hits to contigs within the database. For more information on interpreting BLAST results you should connect to the NCBI BLAST website. Any contigs that match your DNA query sequence can be examined for SNPs by clicking on the blue hyperlink (eg Link to SNPs in BC000010967). This displays the contig and all associated SNPs are displayed in red for ease of identification. The SNP position within that contig is also reported along with information on the SNPs validation status.
- Clicking on the "Contig information" button on the sub-menu will open a page where you can enter a SNP name (a 10 character alphanumeric beginning with 'BS'; e.g., BS00010624) to find out the contig(s) to which it maps, or alternatively enter a contig name (e.g., contig98294) in order to find the SNP(s) that map to it.