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12:34 pm
July 30, 2010
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Razi Khaja
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| posts 6 | |
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Generally, do you find that if a phage genome belongs to a particular cluster or
sub-cluster, that all or most of the phages in that cluster are either circularly
permuted or linearly defined?
For example, from phagesdb.org, I notice that:
5 of 6 genomes belonging to sub-cluster A4 are linearly defined; character of genome
ends for Wile has not been determined (yet).
All 2 genomes belonging to sub-cluster A5 are linearly defined;
All 4 genomes belonging to sub-cluster A6 are linearly defined;
What can be said of the character of genome ends for sub-clusters A1(21 genomes), A2
(12 genomes), A3 (5 genomes)?
What can be said of the character of genome ends for the entire A cluster?
All 4 genomes belonging to sub-cluster B2 are circularly permuted;
All 7 genomes belonging to sub-cluster B3 are circularly permuted;
All 5 genomes belonging to sub-cluster B4 are circularly permuted;
Do you know if all 22 B1 phages are circularly permuted?
All 16 genomes belonging to sub-cluster C1 are circularly permuted.
All 5 genomes belonging to cluster G are linearly defined.
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4:12 pm
July 30, 2010
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Dan Russell
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| posts 44 | |
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Yeah, it's interesting. The clusters almost always have the same end
type/length. Here's what I know:
Cluster A: Almost all 10 bp overhang (the only exceptions are L5 and D29
with 9 bp overhangs, but these may be sequencing errors).
Cluster B: All circ permuted.
Cluster C: All circ permuted.
Cluster D: All circ permuted.
Cluster E: All 9 bp overhang.
Cluster F: All 10 bp overhang.
Cluster G: All 11 bp overhang.
Cluster H: All circ permuted.
Cluster I1: 11 bp overhang.
Cluster I2: 10 bp overhang.
Cluster J: All 4 bp overhang.
Cluster K: All 11 bp overhang except TM4 (10 bp).
Cluster L: All 10 bp overhang.
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12:20 pm
August 26, 2010
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Razi Khaja
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| posts 6 | |
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Post edited 4:50 pm – August 26, 2010 by Razi Khaja
When the genome has defined physical ends, such as for Cluster A where the 3' overhang is almost always 10bp, is the sequence of the 3' overhang always the same: (a) for the entire cluster? (b) for the sub-cluster? or (c) is it always/mostly different?
In other words, what can be said about the similarites or differences between the sequences of the 3' overhangs in a cluster or sub-cluster?
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1:41 pm
August 27, 2010
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Dan Russell
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| posts 44 | |
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Another good question. We've been trying to collect the actual sequence of the 3' overhangs in the database so that we can answer that question more precisely. As of now, however, we've only got <50% of the known overhangs in there, so it's not terribly useful for answering that yet. Hopefully someone will get time soon to enter more.
My gut reaction, having looked at a lot of these, is that they ARE similar within a cluster, and even more similar within a subcluster, but even being in the same subcluster doesn't guarantee precisely the same overhang sequence.
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