BLAT on University of California Santa

        After watching the video 3 that is about the BLAT which is also known as the (BLAST-Like alignment Tool) is the alignment tool used for sequences. This tool also has the ability to align the protein along with the DNA sequence for underlying the genome (Kent, 2002).In the memory when an index of the entire genome is keeps then the BLAT works on the DNA, which is very fast. To determine the sequence that is 95% is greater of similar then the BLAT on the DNA sequences is designed. When we find the sequence of 80% or greater than the BLAT on the protein sequences is designed.

There are following uses of BLAT that is include to

Determine the genomic coordinate of the mRNA and protein in the given assembly;

Finding the exon structure of the gene

Within the full length of the gene displaying the coding regio

From the another species determining the human homologs

        In the base of the granularity when a display is zoomed then the individual of the nucleotides is listed in the base of the position track as shown in the figure 1. In figure 1 you will see the directional arrow that is listing to the left.

Figure 1: Base position Track by Nucleotide

            The configure the sequences of the FASTA format as shown in the table 1 as the submission tool of the BLAT. To display the protein as well as nucleotide sequence the FASTA is the simple text format , for this it has the header line which start by the “.” Along with contains the description and name of the record as shown the forward primer and the reverse primer.

Table 1: Sample of Froward primer & reverse primer