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clustering/distances for unrelated sequences

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Old 12-08-2004, 08:23 PM
Thomas Isenbarger
Posts: n/a
Default clustering/distances for unrelated sequences

I want to use some sort of clustering method (multidimensional scaling
or stochastic proximity embedding, for instance) to group nucleotide
sequences into clouds of similar sequences on a 2-D plot. These methods
require a "dissimilarity matrix", which as far as I can tell is the same
as a distance matrix (high scores mean less similarity).

I have a set of 700+ sequences that I want to group this way, but the

1. contains some homologous groups, but
2. these groups are unrelated, and
3. the sequences are of different lengths

If the sequences were related and could be trimmed to the same length, I
would do an alignment and then use phylip to create a distance matrix,
but since my sequences are unrelated and cannot really be trimmed to the
same length, I am at a loss for what to do.

For a set with so many unrelated sequences of different lengths, the
only thing I have been able to think of is an all-against-all BLAST to
create a score matrix using the normalised bits score, but this gives
high scores for similarities. From there, the only thought I had was to
use the reciprocal of the BLAST score as some perverse measure of

Any ideas?

please email to isen AT plantpath DOT wisc DOT edu

Tom Isenbarger
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Old 12-10-2004, 02:33 AM
Posts: n/a
Default clustering/distances for unrelated sequences

Hi Tom,

You might want to take a look at Pfam and how it was built. They must
have solved similar problems you have.


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Old 12-11-2004, 08:08 PM
Thomas Isenbarger
Posts: n/a
Default clustering/distances for unrelated sequences

she calls her a "real star."

None of the inconsistencies or absurdities I have noted get into
the article. In fact, Smith adds more of her own. As with
Demaris, one of her aims is to make Exner a victim of the press
so that she can imply that the "liberal media" is "protecting"
the Kennedys. As demonstrated above, this is preposterous. Exner
was a media creation used by that press to pummel the Kennedys
who the Times and Post - and their ally the CIA - never liked. To
camouflage this, Smith claims that after her book came out, the
Exners "fled" to California. Yet, according to Demaris, Exner and
her husband were already in California when he met them to start
work on the book. Smith can actually write the Orwellian
statement that Safire - author of no less than five pro-Exner
columns - "derided" Exner's story. Again, contradicting her book,
Exner now says she never went to bed with Giancana. In fact, in
the Vanity Fair version, the whole scene where he proposes to her
is different from the book. In the revisionist go round the
suggestion is that good Italian Catholics, even though they may
be murdering mobsters, don't believe in premarital sex.

More Hidden History

What are the new revelations about the Kennedys that merited
Exner's meeting with Smith for a catered dinner at the five star
Four Seasons Hotel in Newport Beach? There are two. First, she
forgot to add that Bobby's crimefighting campaign was a mirage.

Not only did he not mind JFK's White House meetings with
Giancana, he encouraged her in arranging them. For Vanity Fair,
she remembers RFK's words to her about the subject:
You know I used to be at the White House having lunch or
dinner with Jack, and Bobby would often come by. He'd
squeeze my shoulder solicitously and ask, "Judy, are you
O.K. carrying those messages for us to Chicago? Do you still
feel comfortable doing it?"
This abou

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Old 12-11-2004, 08:13 PM
Thomas Isenbarger
Posts: n/a
Default clustering/distances for unrelated sequences

by Richard Helms and
Harvey. Harvey admitted to the Church Committee that the Edwards
memo was a deliberately false record, a cover story. In fact,
Harvey had already taken over the plots when Edwards told Robert
Kennedy they were terminated.

JFK Never Authorized Them

On the question of authorization, every official from Kennedy's
administration testified that JFK never knew of any plots, or
authorized them. This includes Dean Rusk, Max Taylor, John McCone
(Alleged Assassination Plots pp. 154-161). Even McGeorge Bundy,
about whom many have had suspicions, denied that Kennedy had ever
approved them or been informed of any plots (Ibid. p. 156). To
conclude the matter, the two people in on them at this time
(1962) said the same, i.e. Richard Helms (Ibid. pp. 148-152) and
Bill Harvey (pp. 153-154).

The CIA did try to coax approval from him. The Church Committee
took testimony from two people who were quite compelling on this
point. They were Tad Szulc, a reporter for the New York Times
Washington bureau, and Sen. George

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