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

 

Problem 2

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

Objectives:

  1. Use BLAT to find homologs of a protein, visualize the alignment at the sequence level and in the UCSC genome browser.
  2. Perform the same search using BLAST, compare the search set up and output, and visualize the alignment at the sequence level and in MapViewer.

Objective 1: Find homologs of human hemoglobin subunit beta subunit (NP_000509) in the human genome using BLAT, visualize the alignment at the sequence level and in the UCSC genome browser

Type the accession number NP_000509 in the search box at NCBI (www.ncbi.nlm.nih.gov) and click on the Search button.  Click on the Protein database link and then on the FASTA sequence link.  Copy the sequence and paste the FASTA sequence in the BLAT input page http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Change the Query type to protein and click on the submit button.  Note the hits with good identity scores on chromosome 11.  Click on the details link for the first hit.  Note the alignment on chromosome 11 indicating locations of the exons and introns.  Also, note the alignment of the query amino acid 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.  Note the gene listed in the region (HBB).

Go back to the BLAT search page by clicking twice on the back button of the browser.  Change the Sort output to chrom,start and click on the submit button. Note that all hits are on same chromosome, 11.  Note the START position for the first hit 5225601 and the END position for the last hit 5269678.  Click on the browser link for the first hit.  Change the locations in the position/search box to chr11:5225601-5269678 and click on the Go button.

Note the genes displayed in the view HBB, HBD, HBBP1, HBG1, HBG2 and HBE1. You can obtain more information about these genes by clicking on the gene names. 

Objective 2: Find homologs of human hemoglobin subunit beta subunit (NP_000509) in the human genome using BLAST, compare the search set up and output, and visualize the alignment at the sequence level and in MapViewer.

Go to the tblastn page for the human genome:

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&BLAST_PROGRAMS=tblastn&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=OGP__9606__9558&LINK_LOC=blasttab&LAST_PAGE=tblastn

Paste the accession number NP_000509 in the query box, select the Genome GRCh37.p7 reference assembly top-level database and click on the BLAST button.  If desired, sort the first hit by clicking on the Query start position link. Note the homologs for beta globin.  Click on the Human genome view link near the top above the Graphic Summary and then on the first map element NC_000011 to view the corresponding region and annotation in MapViewer.

You can also run another search using BLASTP.  Go to BLASTP http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&BLAST_SPEC=OGP__9606__9558&LINK_LOC=blasttab

Paste the accession number NP_000509 in the query box, select the RefSeq proteins database and click on the BLAST button. Note the homologs for beta globin.   

For more information about BLAT:

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


 

 

Questions, Comments:  Medha Bhagwat, PhD