Good Morning Jeremy:
I believe you have answered your own question. The contamination
sequences have been removed by the assemblers. They do this by
checking a sequence in question with the contents of all sequences
in genbank. The chrUn sequences in earlier human assemblies should
also be free of contamination, or else it would be unknown contamination.
The newer human assemblies are free of chrUn since the sequence has either
been localized to at least a chromosome, or it was identified as contamination
and been thrown away. I guess you could take the previous chrUn sequences,
break it up into small pieces, and then blat it against current
assemblies. Bits that do not match could be this contamination you
are looking form.
The latest assembly, currently under construction here:
http://genome-test.cse.ucsc.edu/cgi-bin/hgGateway?db=hg19
has a number of unplaced and unlocalized bits that normally would
have been put together into the chrUn. For hg19 we are not
going to place them in chrUn. You will see their names as: chrUn_gl000nnn
take a look here:
http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=hg19&chromInfoPage=
--Hiram
Jeremy Ellis wrote:
> 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
>
>
>
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