Course No. 4 "Sequence Similarity Search: BLAST-Like Alignment Tool (BLAT) "

 

Problem 1

Sequence Similarity Search: BLAST-Like Alignment Tool (BLAT)

Objectives:

1.    Use BLAT to find exon-intron locations of a gene, visualize the alignment at the sequence level and in the UCSC genome browser.

2.    Perform the same search using Basic Local Alignment Search Tool (BLAST), compare the search set up and output, and visualize the alignment at the sequence level and in MapViewer.

Objective 1: Use BLAT to find the exon-intron locations of the human ornithine carbamoyltransferase (OTC) gene using its mRNA NM_000531 sequence, visualize the alignment at the sequence level and in the UCSC genome browser

BLAT requires a FASTA sequence as an input.  Search for NM_000531 at NCBI (www.ncbi.nlm.nih.gov).  Paste the accession number NM_000531 in the search box and click on the Search button.  Click on the Nucleotide database link and then on the FASTA sequence link.  Copy the sequence and paste it in the BLAT input page http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Use all the default options, click on the submit button.  Click on the details link for the first hit.  Note the alignment on chromosome X indicating locations of the exons and introns.  Also, note the alignment of the query mRNA to the genomic sequence in the side by side alignments section. 

Click on the back button of the web browser.  Click on the browser link for the first hit to view the corresponding genome region and annotation in the UCSC Genome Browser. 

Objective 2: Perform a similar search as in Problem 1 using BLAST, compare the search set up and result output, and visualize the alignment at the sequence level and in MapViewer.

Go to the BLAST page http://blast.ncbi.nlm.nih.gov/Blast.cgi and click on the Human link in the BLAST Assembled RefSeq Genomes section.  Note that BLAST provides several databases and can accept the accession number of the sequence.  Enter the accession number NM_000531 in the query box, select the Genome GRCh38.p7 reference assembly top-level database, and click on the BLAST link. 

Note the difference in the output compared to BLAT.  If desired, sort the results by clicking on the Query start position link. 

Click on the Human genome view link near the top above the Graphic Summary and then on the NC_000023 link to view the corresponding region in MapViewer.

For more information about BLAT:

Refer to the article "Using BLAT to Find Sequence Similarity in Closely Related Genomes".

 

Questions, Comments:  Medha Bhagwat, PhD