non-specific primers for human genomic seq

Stephen Baird sbaird at mgcheo.med.uottawa.ca
Tue May 3 19:35:02 EST 1994


Laurent Duret (duret at evoserv.univ-lyon1.fr) wrote:

: In article sbaird at mgcheo.med.uottawa.ca (Stephen Baird) writes:
: > I'm looking for ideas or references on non-specific primers to
: > amplify human genomic sequences. I'd like to amplify small pieces
: > (around 200-500bp) preferably without repetitive elements and
: > preferentially amplify human sequences over any contaminating
: > sequence from bacteria. When doing database searches with small
: > pieces of human genomic sequence like 100-150bp, more often than
: > not the top scores are all human sequences even if the scores are
: > very low. 

: Just be careful. Human sequences represent about 20% of all GenBank sequences, while 
: E. coli sequences represent only 3%.
: So, even with a random sequence, you may expect that similarity search programs will
: find a human sequence much more often than one from any other species.


: However, this does not exclude the possibility of species-specific sequences.


: Laurent Duret
I`ve found the same results with both sequences from bacterial contamination
and drosophila clones. With bacterial sequences the search results are 
dominated with bacteria and with drosophilia sequence queries, the results
are mostly drosophila. There may have been species-specific sequences
in many of these sequences.




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