NCBI BLAST, Mutation Identification & Analysis (SNPs), Lecture 2 Part 3 by Dr. Muhammad Naveed

NCBI, BLAST, Mutation Identification, Mutation Analysis, How to give the name of any mutation? Point Mutation and SNPs.
Using BLAST to identify mutations
An alternative way to search for mutations in your gene of interest is to BLAST the gene sequence. This could be useful if, for example, your gene of interest has an incomplete gene model or no gene model present in the IWGSC CSS assembly. Copy and paste your sequence into the ‘BLAST scaffolds’ box (Fig 1e) and click ‘BLAST’. The result will include:

The visual representation of the query sequence and the hits to the database (Fig 2a).
Table with the BLAST output (Fig 2b). Each row will be a scaffold that shows similarity to the Query input sequence. The scaffolds will either be an IWGSC CSS scaffold (e.g. IWGSC_CSS_5AL_scaff_2810281) or de novo assembled scaffolds with the “UCW_Kronos_U” or “TGAC_Cadenza_U” prefix. These ‘U’ scaffolds consist of de novo assembled reads from the exome capture and sequencing that did not align to any of the IWGSC CSS scaffolds (See Krasileva et al; Supplementary online text section 2.1). Clicking on the scaffold name (Fig 2c) will link to the HSP alignment below (Fig 2d). Beside the scaffold name is a link called “Mutations” which will hyperlink to the HTML output for the EMS mutations in the subject sequence (Fig 2e). This table is the same table that would have been obtained by searching the database using that scaffold name as described above. The E value and length of the Subject sequence are also part of the output.
The High-scoring Segment Pair (HSP) alignment of the Query and Subject sequences. Here the “View Mutations” button will also open up the HTML output for the EMS mutations (Fig 2f).
#MutationAnalysis #BLASTX #Mutationidentifications