LISTSERV 16.0

Help for CILIATEMOLBIO-L Archives

UGA Help Desk

Request a List


CILIATEMOLBIO-L Archives

CILIATEMOLBIO-L Archives


CILIATEMOLBIO-L@LISTSERV.UGA.EDU


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CILIATEMOLBIO-L Home

CILIATEMOLBIO-L Home

CILIATEMOLBIO-L  October 2009

CILIATEMOLBIO-L October 2009

Subject:

update on progress of the MIC genome project

From:

Kathy Collins <[log in to unmask]>

Date:

Sat, 24 Oct 2009 14:43:50 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (72 lines)

Hello Everyone,

For those of you eager to use T. thermophila SB210 MIC genome sequence
information, I offer this update and opportunity to provide feeback.

At the meeting in July, Ed summarized the state of the MIC genome project.
Our first batch of sequence was obtained as paired-end Sanger reads from an
8 kb insert MIC genome plasmid library, with the library and sequencing done
by the JGI through an application to the Community Sequencing Program.  By
the time that JGI actually did the CSP project sequencing, they were phasing
out their Sanger sequencing - instead of the 3X genome coverage, the raw
reads represented less than would be necessary for a good assembly.  To
supplement this sequence and also to complement the bacterial library
approach, Mary Couvillion in my lab made MAC and MIC genome libraries for
Solexa sequencing. We did 95bp reads of paired-end libraries (and shorter
reads of mate-pair libraries that are ultimately not being used). We did the
MAC as a control for the technology, which turns out to have been critical.

Since the July meeting in VT, three members of the bioinformatics core at UC
Davis have been devoting precious time to thoroughly analyze all the data
with rigorous quality control. This has been a highly recursive process,
because the quality of the filtered data impacts how to use it in mapping
and analysis, and then results from mapping impact how the data should be
filtered, and back and forth and back and forth. They are doing a stellar
job in return for relatively little compensation, as there isn't an official
source of funding for the project.

It turns out that much of the sequence data, both Sanger and Solexa, is poor
quality and/or uneven in distribution across the MAC genome.  The high AT
content is problem, as recent publications from large genome centers attest
(Plasmodium has comparable AT and has been a challenge to sequence and
assemble).  There are new Solexa methods that increase sequence quality and
help reduce the coverage bias, but for now we're concentrating on using the
data in hand.

The numbers for MIC genome size generated right before the meeting, without
the recursive process of filtering the data and evaluating the mapping
statistics, overestimated the amount of sequence that is likely to be
MIC-specific. It seems that the MIC has more MAC-destined DNA than
MIC-specific DNA. The strategy for candidate IES mapping has been evolving,
successfully. We are still deciding what to analyze about the candidate IES
sites as a large set - how much do we care about position relative to
predicted ORFs? We only nucleotide resolution for IES sites mapped from the
Sanger reads. The larger number of Solexa paired-end reads also defines IES
with some caveats, based on the false positive rate of IES detection in the
MAC library. There will be tracks in a genome browser that will let everyone
search for candidate sites based on increasing weight of evidence.

Before this gets too long, I need to come to the promise that I made to
several of you at the meeting, which was to make a sequence file of bona
fide MIC-specific DNA that one could use to design experiments. The Sanger
reads that have been filtered stringently for quality yet don't map to the
MAC are the best source of reliable MIC-specific sequence, but the volume of
sequence will be only a fraction of the total MIC-specific content (there is
much more sequence coverage in the Solexa reads, but we can't seem to filter
the junk out as reliably). As of yesterday, the plan is to generate one file
of Sanger reads with apparent MIC sequence content and another file with the
subset of apparent MIC sequences that can be LINKED to a region of the MAC.
 This second file will also attempt to assemble IES scaffolds (this process
will be highly incomplete).

Here is the question, for anyone intending to use the MIC-specific sequence
file as soon as it is available: Is is more useful to have a few IES fully
assembled or to have a larger data set of thousands of partial IES linked at
some distance to a region of the MAC? Or is is most important to have the
IES junction sequences? Or is the MIC-specific sequence without linking
information adequate?  I know all these things are interesting to analyze on
genome scale, but that's not within the scope of the current project. The
question is in the context of immediate use by the community for ongoing
experiments.

Kathy

Top of Message | Previous Page | Permalink

Advanced Options


Options

Log In

Log In

Get Password

Get Password


Search Archives

Search Archives


Subscribe or Unsubscribe

Subscribe or Unsubscribe


Archives

November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
June 2019
May 2019
April 2019
March 2019
February 2019
December 2018
November 2018
October 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
December 2017
November 2017
October 2017
September 2017
August 2017
May 2017
April 2017
March 2017
January 2017
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
September 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
September 2014
August 2014
July 2014
May 2014
April 2014
March 2014
January 2014
December 2013
November 2013
October 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
September 2012
July 2012
June 2012
May 2012
April 2012
March 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
March 2011
February 2011
January 2011
December 2010
November 2010
September 2010
August 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
December 2006
November 2006
October 2006
September 2006
August 2006
June 2006
May 2006
March 2006
February 2006
January 2006
December 2005
November 2005
October 2005
August 2005
July 2005
June 2005
May 2005
April 2005
March 2005
February 2005
January 2005

ATOM RSS1 RSS2



LISTSERV.UGA.EDU

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager