BLAST practice

1. Links to several different nucleotide sequences are given below. Read the rest of the instructions before continuing.

List of sequences 1  2   3   4   5   6   7   8    9   10    11   12   13   14   15   16

2. Use the mouse to highlight your sequence.

3. Copy the sequence.

4. Use BLAST to identify your sequence as shown in the BLAST tutorial. Refer back to the tutorial if you have questions.

5. Some questions that might be asked about nucleotide sequences are listed below. See if you can answer any of the questions from your results.

Questions that might be answered from a BLAST search

1. How long is the sequence that you used to search the database?

2. What is the most likely identity of this sequence? What data supports this conclusion?

3. What organism is the source of the sequence? What is the common name for this organism?

What phylum contains this organism?

What is the accession number for this sequence?

Is this sequence expressed? How do you know?

If your sequence is expressed, where (tissue) and when is it expressed?

Is anything known about factors that cause your sequence to be expressed?

4. How many sequences can you find with an E value less than 0.05?

What organisms did those sequences come from?

5. Look at the first matching sequence, how long is the extent of the alignment and what fraction of the nucleotides match?

6. Use PubMed to find the possible function of the protein specified by your DNA sequence. Describe what's known about the role of this protein in the organism that provided the DNA.