BLAST Practical
Objectives:
1. Understand the fundamentals of BLAST.
2. Determine the taxonomic position of a given sequence.
3. Use NCBI BLAST to compare sequences with those stored in the database.
Procedure:
1. Open the file "sequence.txt" located in the desktop folder containing the course files. The file is in FASTA format. The first line (beginning with a ">" symbol) provides a description, followed by the sequence.
2. Visit the NCBI BLAST website: http://blast.ncbi.nlm.nih.gov.
3. Under “Basic BLAST,” select the “nucleotide blast” option to access the nucleotide BLAST input form.
4. In the "Enter Query Sequence" section, click the “Browse” button to upload "sequence.txt" from the course folder.
5. Under "Choose Search Set," select the option for "Others (nr, etc.)."
6. Click the blue "BLAST" button in the bottom left corner.
7. With the guidance of your instructor, analyze the four sections of the BLAST output: the Header, Graphic Summary, Descriptions, and Alignments. Identify the closest match to your unknown sequence and evaluate the strength of the match. Consider whether the match is due to genuine sequence homology or simply a chance occurrence.
Results and Evaluation:
1. Snapshot of BLAST search: Paste a screenshot of your BLAST results below.
2. Closest match to the unknown sequence:
3. Criteria for selecting the best matching sequence: List the criteria you used to identify the most accurate match for your sequence.
4. True sequence homology: Explain whether the match is likely due to genuine homology or if it could have occurred by chance. Provide reasoning.
