KSH 0601

Bioperl and BLAST

 

BLAST (Basic Local Alignment Search Tool) is a representative analysis program which analyzes the homology between two genes by aligning and comparing the two sequences of amino-acid or DNA.

Use of BLAST (source: https://en.wikipedia.org/wiki/BLAST)

1. Identifying species

2. Locating domains

3. Establishing phylogeny (Create a phylogenetic tree)

4. DNA mapping

5. Comparison

 

Kinds of BLAST

1. nucleotide blast (blastn) - comparison between a given DNA sequence and the most similar DNA sequence from the DNA databases such as GenBank

2. protein blast (blastp) - comparison between a given protein sequence and the most similar protein sequence from the protein databases such as PIR or SwissProt

3. blastx - nucleotide to protein converter

4.. tblastn - protein to nucleotide converter 

5. tblastx - homology comparison of nucleotide sequences by translating the sequences into proteins

 

How to use BLAST

1. Go to the webpage, "www.ncbi.nlm.nih.gov/"

2. Click "BLAST" button on the right side

3. Choose a BLAST program which you want to run.

4. Upload your sequence file by clicking "Browse" button or write down the Accession number(s) and GI(s) or FASTA sequence(s) from the GenBank data

5. Click "BLAST" button

 

Ex) Search BRCA1 gene which is a human tumor suppressor gene  from ncbi GenBank data