Tel Aviv University Department of Computer Science
Fall 2001-02
Algorithms in Molecular Biology 0368.4020.01 Ron Shamir
Class bulletin-board
Thu, 22 Nov 2001, Book containing scribes of last course is available
at Safrut Zola
Tue, 13 Nov 2001, Roded
Q1: Start codon is AUG (the input is mRNA). By definition in a reading frame
each triple is treated as a codon (no other nucs). You may not assume that
a start codon comes right after a stop codon (in an operon).
Q2: Left as an ex.
1.This question refers to one reading frame (one of six) :
Can I make these assumptions:
1.1.The start codon is "ATG".
1.2.The gene of prokayotes includes only triplets of encoding
nucleotides and no others (singles or doubles) nucleotides.
For example, is this gene in operon mRNA molecule is
legal: "[ATG]A[CAT][UGA]" (where "ATG" is the start codon,"UGA" - stop
codon, "CAT" is codon included in the gene and A is a single nucleotide which
not encodes).
1.3. Can I assume that after each stop codon the new gene
starts, i.e. the next triplet of nucleotides is the start codon of the next
gene? For example, is this seq. is legal or not:
"...[UGA][CAT][ATG]..."(where "UGA" - stop codon of the gene and "ATG" is the
start codon of the next gene)?
Note: I know that prokayotes don't include introns and exons, so it has
to include only encoding codons without "junk"(so after the stop codon of the
gene the start of the new gene must appear and nothing can appear between
them.Is it right?) I read in book that it is not allways this way.
2.Now the question about the downstream of the DNA:
If the start codon is "ATG", what is the start codon in the second strand of
the DNA?
Is this "TAC" (complement of "ATG") and then two genes start simultaniously.
Or maybe it is "ATG" too. Or maybe it is complement and reverse of "ATG" -
"CAT"? The same questions about stop codons...
Sun, 11 Nov 2001, Roded
Submission of Ex1: delayed till strike ends. You can submit both at
the lecture and directly to me (my mailbox is on floor 1).
Q2: genes are recognized (in here) only by their start and end codons.
No two genes in the same reading frame can share any codon
(meaning they do not overlap)
Q3: The linear alg. returns yes/no.
Hi,
I have some questions regarding the exercise 1...
first, administrative information:
do we submit the exercise at the lecture?
if a strike continues and there won't be a lecture -
do we submit it at the next lecture?
can you please add a link on the course webpage that
will inform us atleast 12 hours before the lecture
-will you give a lecture or not.
speaking of the webpage - I didn't succeed to dowlnoad
even one file among all the links in the table... can
you do something about it?
second, I have an understanding problem in question 2
(probably I didn't get something with the biology
introduction):
can I recognize the start and end of genes only by
"start" and "stop" substrings (in the algorithm)?
does each gene always start with a "start" substring
and stop with a "stop" substring?
when genes overlap, does it mean that first I see a
"start" of the first gene, then a "start" of a second
one, and only then "stops" will follow in any order?
may one "start" start both overlapping genes?
may one "stop" stop more then one gene?
when you are saying "two or more genes may overlap,
but not in the same reading frame", do you mean that
if two genes overlap, then they must start and stop in
two different frames?
in question 3:
can I assume that the linear algorithm I have (which
determines whether S is a subsequence of T) returns an
index in T where the similarity starts?
Sorry, I know it's a lot of questions, but as there is
no other way but to bother you...
Thanks,
Yevgeny.
