BLAST LAB
Use NCBI BLAST tools to analyze the following DNA that you just sequenced from a
plasmid and answer the following questions:
GGGCGAATTGGGCCCGACGTCGCATGCTCCCGGCCGCCATGGCCGCGGGATA
CGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTCGCTCCCCAACGCTT
TCGCTCCTCAGCGTCAGTTACTGCCCAGAGACCCGCCTTCGCCACCGGTGTTC
CTCCTGATATCTGCGCATTCCACCGCTACACCAGGAATTCCAGTCTCCCCTGC
1. Use VecScreen (http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html) to identify
if there is vector contamination. If there is contamination, what is it?
2. Trim out any offending contamination and do a Nucleotide-nucleotide BLAST
(blastn) (http://www.ncbi.nlm.nih.gov/BLAST/) search with the good stuff.
(a) The highest scoring BLAST hit is to what organism?
(b) What is the gene?
(c) Who submitted the sequence and from what institution?
(d) Get the following data for the “hit” - E-value: Identities:
FOR YOUR PROJECT
Do a short write up (1-2 pages) with the following outline...
Title
Materials and Methods
- include everything that you needed to complete project
- PCR, DNA isolation, bioinformatics, etc
Results
- make a table of results
Sequence Identification
Appendix
- sequences
Name of closest hit
% identity