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SNP annotation using BLAST
A BLAST search against dbSNP produces output similar to a regular nucleotide BLAST search against NCBI. However, when searching against dbSNP, The Workbench also offers the user the possibility to transfer the found BLAST hits to the query sequence as variation annotation. This information can then be used to interpret experimental data or to design further experiments using either the primer designer functionality or the cloning editor of the program.
SNP BLAST search parameters
First you choose the species and database for use in the BLAST search. Then you can set parameters for the BLAST search as shown in the below illustration. The top part of the parameters shown in the illustration pertains to the BLAST algorithm. In the lower part are two parameters pertaining to how variation annotation is transferred to the query sequence:- Max no of mismatches. The maximal number of mismatches found in the alignment between the query sequence and a hit in dbSNP for a variation annotation to be added. Since entries in dbSNP always have at least one ambiguity character this parameter is constrained to always have at least this value. If the objective is to include insertiondeletion polymorphisms it is necessary to increase this parameter to at least the desired insertion-deletion size.
- Min length of alignment. The minimum number of residues which must be aligned between the query sequence and a dbSNP hit for a variation annotation to be added.
Next you can choose how the output of the SNP BLAST should be displayed. There are three options as shown in the illustration.
- Show result as graphics. This will show a graphical view of the BLAST hits as known from the other BLAST searches.
- Show result as table. This will show a tabular view of the BLAST hits as known from the other BLAST searches.This and the above view allow the user to inspect the result of the BLAST search and in both views it is possible to download the sequences from dbSNP
- Add annotations to input sequences. This will add the SNP annotations found in the BLAST search to the sequence that was chosen in the first step. If multiple sequences where selected, a BLAST search is conducted for each of the sequences.
Result of SNP BLAST
The results of the SNP BLAST search can be examined through either the graphical or tabular view of the BLAST search, and also as annotations on the query sequence.The SNP BLAST hits
The graphical BLAST output of a dbSNP search is shown in the illustration on the right. If the option of annotating with variation annotation was chosen, the query sequence in the BLAST search object is also annotated with the dbSNP hits which passed the set criteria. In the graphical editor auxiliary information about the hits are shown in a tooltip when the mouse hovers on a hit sequence. In addition to the BLAST statistics, it includes the length of the original dbSNP sequence, the variation position, the database build and the type of variation. This information is also available from the tabular view of the BLAST search.The SNP annotations on the sequence
When sequences are annotated with variation information as shown in the above illustrations the type of variation is displayed in the name of the annotation. Furthermore, if genotype information is available it can be accessed in the tooltip shown when the mouse hovers on the annotation.Read more about SNP in our Bioinformatics explained: Single-Nucleotide Polymorphisms
