program to detect chimeric pcr artefacts

Brian Foley btf at
Wed Dec 3 11:01:30 EST 1997

Bruce J. Turner wrote:
> I would appreciate information on programs to detect chimeric 
> pcr artefacts that might be formed when amplifying a multigene 
> family with primers prepared to common conserved regions...

	The RIP "Recombinant Identification Program", available
from the Human Immunodeficiency Virus Sequence Database,
was designed to detect recombinant forms of HIV, but could easily 
be used for other problems, such as the one you refer to.
Source code in C and a SUN-OS executable are prvided.
	RIP needs a "background alignment" on non-recombinant
gene (or protein) sequences, labelled A B C etc... (The program
could be modified to accecpt more descriptive names, it was
written for the subtypes of HIV, which are just designated
A B C etc...).
	The user must then align their sequence to this 
"background alignment", and set the window size and other
parameters (or go with dfault values).  
	RIP uses a sliding window and in each window checks to
see if the sequence in question is most similar to one of the
background sequences.  A recombinant should be most similar to 
one background sequence over some region(s) of the sequence, 
and most similar to another background sequence (or to none)
over other region(s).  More details are provided on the
RIP www page.

	RIP can produce a graphical output, which shows not
only how similar the query sequence is to each of the background
sequences, but also indicates regions where the background
sequences are so similar to each other (highly conserved
regions) that one cannot expect to differentiate between the
different backgrounds.

	In some cases, one must be careful to assess the
possibility that a "recombinant" may not truly be recombinant,
but instead reflects evolutionary conservation of some regions
of the sequence, while other regions diverge.  With HIV, we
know that different gene regions evolve at different rates, and
that the rates are variable in different lineages of this 
|Brian T. Foley               btf at                       |
|HIV Database                 (505) 665-1970                         |
|Los Alamos National Lab     |
|Los Alamos, NM 87544  U.S.A. |

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