Hiram and All; I appreciate the responses. I am interested in the bacterial contamination sequences as indicated here in section VI: > http://www.ncbi.nlm.nih.gov/genome/assembly/assembly.shtml
It states: "contamination: All assemblies should be screened for foreign and vector sequences. The source of these foreign sequences can range from bacterial genome contamination (due to propagating clones in bacteria) to contamination from other projects being sequenced at a particular sequencing center." Not all of these contaminant sequences would be from the bacteria that the clones were propagated with, but there are likely sequences from normal bacterial/organismal flora from the donor human that were cloned and sequenced as well (not to mention purely random genomic fragments from a wide variety of sources (pollen, water contamination, etc). I have looked through ChrUn from both hg16 and hg15 (hg17 and 18 do not have the ChrUn data) and there does not appear to be any of the bacterial contaminant sequences in this data (it looks like it is information from rare PCR products and other cloning artifacts). So, my question is simply, "Where are the non-human contaminant sequences?". I hope this clarifies my question. Jeremy On Apr 1, 2009, at 4:57 PM, Hiram Clawson wrote: > Good Afternoon Jeremy: > > You may find the following discussion of interest: > > http://www.ncbi.nlm.nih.gov/genome/assembly/assembly.shtml > > >> Jeremy Ellis wrote: >>> Hello all again. I appreciate the responses I had for my first >>> question and they helped. I have been looking through ChrUn from >>> the earlier assemblies and I now realize that this isn't quite >>> what I expected. Most of these sequences (so far) appear to be >>> odd human- like sequences due to a variety of probable reasons >>> (PCR/cloning artifacts, etc). I think that the sequences I am >>> interested in is the stuff that might have been thrown out as it >>> appeared to be a contaminant sequence from bacteria, fungi, or >>> water borne protozoa, etc. Would these sequences have been long >>> since disposed of and ignored or could there still be hope for >>> me in finding a treasure trove of "garbage" sequence? >>> >>> Thank you again for your help! >>> >>> J. > Jeremy Ellis [email protected] 949-824-1223 Arora Lab Developmental and Cell Biology University of California, Irvine _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
