A. Your name
B. Bioinformatics
by David Mount, a suggested text for the course, hasn't played much of
a role thus far, but it could for many of the scenarios from here on out,
and it would be useful for us to know whether people in the course have
the book in hand. Do you have a copy of the book?
B. Were you able
to download the set of proteins from E. coli K-12 and from one of
the two pathogenic E. coli to your own computer?
C. Were you able to run FormatDB
to create a database of proteins from E. coli K-12?
D. Were you able to run BlastAll
to compare the set of proteins of the pathogenic strain against the database
of K-12 protein, producing a file with a size of about 40 megabytes?
E. Were you able to examine
a portion of the output of the program by using DR (or by any other means)?
| Comments for questions II.A
through II.E: |
|
A. Do you know where
to find each of the seven items listed in the notes (e.g. Query name) in
the output from Blast?
B. Do you know where each
of the seven items in the output of BlastParser comes from?
C. Were you able to modify
and run BlastParser so that it opened the file you created with
BlastAll? (If you couldn't, make sure that you downloaded BlastParser
into
the same directory as the output from Blast, presumably /Blast, and that
you are in that directory when you try to run the program)
| Comments for questions III.A
through II.C: |
|
A. How comfortable
are you with interpretting and using character classes in regular expressions,
to the extent that they are used in Blast Parser? Example:
my ($query, $query_description) = /^Query=\s+(\w+)\W+(.+)/;
B. How comfortable are you
with interpretting and using repetition symbols in regular expressions,
to the extent that they are used in Blast Parser? Example:
my ($query, $query_description) = /^Query=\s+(\w+)\W+(.+)/;
C. How comfortable are you
with interpretting and using expressions that capture matched patterns,
to the extent that they are used in Blast Parser? Examples:
my
($query, $query_description)
= /^Query=\s+(\w+)\W+(.+)/;
$subject_description
= $3;
D. How comfortable are you
with the concept of arrays, to the arrays are used in Blast Parser?
Examples:
@query_info
= ($query, $query_description, $query_length);
push @query_info,
$subject_name, $subject_description, $subject_length,
$expectation;
my $result_line
= join("\t", @query_info); # "\t" = tab character