Re: briggsae BACs

John Spieth jspieth at watson.wustl.edu
Tue Oct 7 22:33:44 PDT 2003
Hi Eric,

This is in my hands now.  Jim send me the briggsae BAC end sequences and we are going to
map these onto the briggsae sequence so one can determine on which briggsae BAC their
favorite gene can be found.  I've been slow in making sure the BACs are actually
available - no sense mapping them if they can't be sent out.  I've finally determined
they are available for distribution and will get the BAC end sequences out so they can
be mapped.

Sorry for the delay,

John



> Dear Jim and other fellow briggsae folk,
>
> Last month it seemed that major progress was made in identifying
> which BAC ends went together to form  briggsae sequence scaffolds,
> and perhaps some progress as well in determining who physically has
> said BACs (see old thread below).  But I'm not sure where it all
> stands now.  Can anyone update us?  The ultimate goal, if you recall,
> was to be able to deduce from WormBase or some other public server
> which clones cover a region of interest, and then be able to obtain
> one or more of them for experiments.
>
> Thanks,
>
> Eric
>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>                                            Eric S. Haag, Ph.D.        ~
>    Assistant Professor                                   ~
>    Department of Biology                               ~ ~
>    University of Maryland
>    College Park, MD  20742               ~                       ~   ~
>    phone:  (301) 405-8534	fax:  (301) 314-9358        ehaag at wam.umd.edu
>   http://www.life.umd.edu/biology/faculty/haag/index.html	  ~         ~

>                                      "I'd rather be here now."
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>
>
> At 11:22 AM -0400 9/5/03, Jim Mullikin wrote:

>>Hi,
>>Just catching up on this thread...
>>
>>I have put the following files here:
>>
>>ftp://ftp.nhgri.nih.gov/pub/outgoing/mullikin
>>
>>
>>cb25.agp8.RPCIpos       953 KB          9/5/2003        3:09:00 PM
>>cbrigBACendsCLIP.fasta.gz       3195 KB         9/5/2003        3:09:00 PM
>>cbrigBACendsCLIP.fasta.qual.gz  6249 KB         9/5/2003        3:10:00 PM
>>
>>The BACend reads are in cbrigBACendsCLIP.fasta
>>
>>I used ssaha to align these reads to cb25.agp8.fasta that I downloaded from:
>>ftp://ftp.sanger.ac.uk/pub/wormbase/cbriggsae/cb25.agp8
>>
>>THe cb25.agp8.RPCIpos file has five columns:
>>(Scaffold name, RPCI read name, Alignment start in scaffold,
>>Alignment end in scaffold, Orientation)
>>
>>E.g.:
>>
>>grep fpc0129 cb25.agp8.RPCIpos | head
>>
>>        cb25.fpc0129      RPCI94_08D06.T7       4541       5086 -
>>        cb25.fpc0129     RPCI94_27F10.SP6     124221     124706 +
>>        cb25.fpc0129     RPCI94_22P22.SP6     124222     124829 +
>>        cb25.fpc0129      RPCI94_11J07.T7     129659     130218 +
>>        cb25.fpc0129      RPCI94_09G18.T7     129666     130257 +
>>        cb25.fpc0129      RPCI94_21J08.T7     148196     148683 +
>>        cb25.fpc0129     RPCI94_03B04.SP6     162079     162630 -
>>        cb25.fpc0129     RPCI94_26E21.SP6     162760     163365 +
>>        cb25.fpc0129      RPCI94_17N14.T7     171080     171658 +
>>        cb25.fpc0129      RPCI94_26E21.T7     172696     173271 -
>>
>>Hope this helps, and that the browser groups can load this information.
>>
>>Thanks,
>>Jim
>>
>>
>>John Spieth wrote:
>>
>>>You're so smart!! I'll ask around about the BAC end sequences and see if we
>>>can get them mapped to the assembly and displayed in WormBase some how.
>>>
>>>thanks,
>>>
>>>John
>>>
>>>
>>>On Thursday 04 September 2003 08:17 pm, Jacquie Schein wrote:
>>>
>>>>Hi John,
>>>>
>>>>Are the BAC end sequences available as a set on their own? It would
>>>>then be a relatively simple matter of BLASTing BACs with paired ends
>>>>against the assembly (or the contig that's of interest) and determine
>>>>which BACs cover the gene based on their end coordinates. You
>>>>wouldn't have to dig up all the reads that went into the contig, then.
>>>>
>>>>Regards,
>>>>Jacquie
>>>>
>>>>
>>>>----- Original Message -----
>>>>From: "John Spieth" <jspieth at watson.wustl.edu>
>>>>To: "Jacquie Schein" <jschein at bcgsc.ca>; "Marco Marra"
>>>><mmarra at bcgsc.bc.ca>; <susan.mango at hci.utah.edu>; <jschein at bcgsc.bc.ca>
>>>>Cc: "Joanne Nelson" <jnelson at watson.wustl.edu>;
>>>><mullikin at nhgri.nih.gov>; "Eric Haag" <ehaag at wam.umd.edu>;
>>>><aillie at sfu.ca>; <bpgupta at its.caltech.edu>; "WormBase dev"
>>>><wormbase-dev at wormbase.org>
>>>>Sent: Thursday, September 04, 2003 5:43 PM
>>>>Subject: Re: briggsae pha-4
>>>>
>>>>>Hi Jacquie,
>>>>>
>>>>>Thanks for the tip. The clue here is figuring out which BAC ends were used
>>>>>for each contig and where they map in the contig. I'm sure this information
>>>>>is available in the assembly. I would guess that Jim Mullikin has
>>>>it. Maybe this is information that should be in WormBase. Notice that the
>>>>number of people interested in this has grown since my first email to Susan
>>>>earlier today. Eric Haag wrote just after I emailed Susan. My guess is
>>>>more people will be after this kind of information in the future.
>>>>>
>>>>>thanks,
>>>>>
>>>>>John
>>>>>
>>>>>
>>>>>On Thursday 04 September 2003 07:20 pm, Jacquie Schein wrote:
>>>>>
>>>>>Pieter de Jong might have BAC filters from the briggsae BAC
>>>>>library (RPCI-94; http://bacpac.chori.org/cbriggsea94.htm).
>>>>>Alternatively, if the BAC end sequences identify a suitable BAC or BACs that
>>>>>span the gene, you could simply order the individual BACs from Pieter.
>>>>>>
>>>>>>Hope that helps.
>>>>>>
>>>>>>Jacquie
>>>>>>
>>>>>>
>>>>>>----- Original Message -----
>>>>>>From: "Marco Marra" <mmarra at bcgsc.bc.ca>
>>>>>>To: <jspieth at watson.wustl.edu>; <susan.mango at hci.utah.edu>;
>>>>>><jschein at bcgsc.bc.ca>
>>>>>>Cc: "Joanne Nelson" <jnelson at watson.wustl.edu>;
>>>>>><mullikin at nhgri.nih.gov>
>>>>>>Sent: Thursday, September 04, 2003 4:34 PM
>>>>>>Subject: Re: briggsae pha-4
>>>>>>
>>>>>>The briggsae fosmid / BAC grids were put together in collaboration
>>>>>>with the now-defunct Genome Systems, formerly of St. Louis. Genome
>>>>>>Systems was offering them for sale, but was purchased by Incyte I think.
>>>>>>One could explore with Incyte whether they offer the grids.
>>>>>>++++++++++++++++++++++++++++++++++++++++++
>>>>>>Marco A. Marra, Ph.D.
>>>>>>Director,
>>>>>>Genome Sciences Centre.
>>>>>>British Columbia Cancer Agency,
>>>>>>600 West 10th Avenue, Room 3427
>>>>>>Vancouver, British Columbia, Canada V5Z-4E6.
>>>>>>
>>>>>>mmarra at bcgsc.bc.ca
>>>>>>www.bcgsc.bc.ca
>>>>>>
>>>>>>604-877-6085 - FAX
>>>>>>604-877-6084 - FRONT OFFICE
>>>>>>604-877-6082 - OFFICE
>>>>>>++++++++++++++++++++++++++++++++++++++++++
>>>>>>
>>>>>>
>>>>>>>----- Original Message -----
>>>>>>>From: "John Spieth" <jspieth at watson.wustl.edu>
>>>>>>>To: <susan.mango at hci.utah.edu>
>>>>>>>Cc: "Joanne Nelson" <jnelson at watson.wustl.edu>;
>>>>>>
>>>>>><mmarra at bcgsc.bc.ca>;
>>>>>>
>>>>>>><mullikin at nhgri.nih.gov>
>>>>>>>Sent: Thursday, September 04, 2003 4:10 PM
>>>>>>>Subject: briggsae pha-4
>>>>>>>
>>>>>>>>Hi Susan,
>>>>>>>>
>>>>>>>>Your inquiry to Alan Coulson in mid-July ended up on my desk
>>>>>>>>yesterday. I'm not exactly sure how it made it's way here or why it
>>>>>>>>took so long, but I'm sorry if no one has responded to you about
>>>>>>>>this. 
>>>>>>>>
>>>>>>>>The briggsae contig, cb25.fpc0129, came from the assembly of whole
>>>>>>>>genome shotgun reads and BAC end reads. This assembly was done by
>>>>>>>>Jim Mullikin using the Phusion assembler. Jim might be able to
>>>>>>>>tell you which plasmid reads and BAC end reads went into this
>>>>>>>>contig but I don't have anyway of knowing. I've CC'd Jim on
>>>>>>>>this so he may be able to tell you more. I think most
>>>>>>>>of the plasmid clones from the GSC were kept but Sanger
>>>>>>>>also sequenced about half of the plasmids and I don't know if
>>>>>>>>they kept theres. This is something we can find out. I believe all 
>>>>>>>>the BACs are available but will have to check on that to be sure.
>>>>>>>>I really think your best bet for getting briggsae pha-4 is to
>>>>>>>>PCR some of it out of briggsae DNA and use that as a probe against 
>>>>>>>>a grid of briggsae fosmids, if such a thing exists. I think it does but 
>>>>>>>>the one to know for sure is Marco Marra, whom I've also CC'd on this.
>>>>>>>>
>>>>>>>>Sorry I've not been more help. If you have additional
>>>>>>>>questions or I've not been clear, please don't hesitate to contact me.
>>>>>>>>
>>>>>>>>Regards,
>>>>>>>>John
>>>>>>>>
>>>>>>>>John Spieth
>>>>>>>>Genetics, WormBase and
>>>>>>>>The Genome Sequencing Center
>>>>>>>>Washington University School of Medicine
>>>>>>>>4444 Forest Park Blvd, Box 8501
>>>>>>>>St. Louis, MO 63108
>>>>>>>>Email: jspieth at watson.wustl.edu
>>>>>>>>Phone: (314) 286-1840
>>>>>>>>FAX: (314) 286-1810
>>>>>>>>WormBase: [http://www.wormbase.org]
>>>>>>>>The Genome Sequencing Center: [http://genome.wustl.edu/]
>>>>>>>>