Due: Mar. 2, 2010 MCB 432 Name __key________________
Assignment 4 20 points total
Analyzing Sequences Using NCBI BLAST
(http://blast.ncbi.nlm.nih.gov/Blast.cgi)
Data for the Assignment
This assignment explores some basic BLAST analyses using the NCBI WWW Server. A summary of
some elements can be found at: http://www.ncbi.nlm.nih.gov/blast/about/. Pay attention to the details.
In particular, read the entire BLAST Forms section of the page. How you use BLAST (or any other
tool) matters.
Data for the Assignment
The data for this assignment are available in electronic form from the class WWW server. The data are
in the Assignment 04 directory: http://www.life.uiuc.edu/mcb/432/Assignments/04/, or you can find
links to the file on the Schedule page: http://www.life.uiuc.edu/mcb/432/Schedule.html
The file pep1.txt is a plain text files with a peptide sequence in FASTA format.1 Your goal is to identify
the function of the protein, and what organism it is from.
Using BLAST to Find Sequences Similar to a Protein
Go to the NCBI BLAST Home page: http://blast.ncbi.nlm.nih.gov/Blast.cgi.
Our first step in our quest to identify pep1 and its source organism is to use the blastp program to search
for similar sequences in the nr (non-redundant) protein database.
Follow the link from the BLAST Home page to "protein blast".
1. Associated with the Query Sequence box is a question mark icon. Click on the icon to reveal its
text box, which ends with "more...". Click this link for a detailed description of the input
formats. Review the information and answer the following:
1a. What are the 3 different types (formats) of input acceptable to the BLAST programs?
2 pt FASTA
Bare Sequence
[Sequence] Identifier
1b. What does "K" stand for in a nucleotide sequence? 1 pt G/T [might include (keto)]
1c. What does "K" stand for in a protein sequence? 1 pt lysine
1d. What does "U" stand for in a nucleotide sequence? 1 pt uridine
1e. What does "U" stand for in a protein sequence? 1 pt selenocysteine
Use your computer web browserr's Copy and Paste functions to paste a copy of the pep1 definition and
sequence into the Enter Query Sequence box. Check that the following setting are set (most, but not all,
will be the default value): Database, Non-redundant protein sequences (nr); Algorithm, blastp; Max
target sequences2, 500; Short queries, Automatically adjust ...; Expect threshold, 10; Word size, 3;
Matrix, BLOSUM62; Gap Costs, Existence: 11 Extension 1; Compositional adjustments, Conditional
compositional score ...; Filter, unchecked; and Mask, both choices unchecked.
1 FASTA format if defined by having a line that starts with a greater than sign (>) and the description of
the sequence. All remaining lines to the end of the file, or the next line that starts with a greater than
sign (>), is interpreted as sequence. Most programs that accept a FASTA format file will allow blank
spaces in the lines with sequence data.
2 If you do not see this of the parameters that follow, click the arrow next to "Algorithm parameters to
reveal these settings. Remember this in future exercises.
