9Je11
Genome helpers:
(1) Vanessa's directions worked on the first go!! but a bit more help pls:
(2) My browser allows me to copy, but I need to paste into EXCEL and forgot how
to convert FASTA to EXCEL so I can xck that all DMIT
are included: pls provide these steps (copy/paste into EXCEL)
(3) In MS I need to cite a URL or some other BRIEF address; i.e., though I can
get the amplified sequences, I am writing the MS for
others to use my results-conclusions, perhaps access the same DMIT data
(amplified sequences)- WHAT SHOULD I STATE for a refcitation?
I don't think I should give all Vanessa's directions into a refcitation
As always, thanks to all who helped- watch for a MS later (with soe.ucsc in
ACKNOWLEDGEMENTS)
Gratefully,
A
> Date: Thu, 9 Jun 2011 16:48:19 -0700
> From: [email protected]
> To: [email protected]
> CC: [email protected]
> Subject: Re: [Genome] mouse microsatellite DMIT amplified sequences
>
> Hi Ann,
>
> The table browser (http://genome.ucsc.edu/cgi-bin/hgTables?command=start)is
> the tool that you will need to use to obtain the sequences for the DMIT loci.
>
> While in the table browser set the following:
>
> clade: mammal
> genome: Mouse
> assembly: July 2007 (NCBI31/mm9)
> group: Mapping and Sequencing Tracks
> track: STS Markers
> table: stsMapMouseNew
> region: genome
> filter: click on "create". At the bottom of the page, enter the following
> into the Free-form query section:
> name like "%D%MIT%"
> Click "submit".
> output format: sequence
>
> Click "get output"
>
> Click "get sequence"
>
> This will provide you the sequences for all of the DMIT loci.
>
> If you have further questions, please email the mailing list at:
> [email protected].
>
> Vanessa Kirkup Swing
> UCSC Genome Bioinformatics Group
>
> ----- Original Message -----
> From: "ann eileen miller baker" <[email protected]>
> To: [email protected]
> Sent: Thursday, June 9, 2011 11:11:22 AM
> Subject: Re: [Genome] mouse microsatellite DMIT amplified sequences
>
>
> 9Je11
> Sorry to be unclear: the JAX site has an old (before the mouse genome
> sequenced)
> list of DMIT amplified sequences with many "N" (can not score accurately a
> given base).
> I am trying to get the list of amplified sequences for all DMIT loci
> (microsatellite loci).
> Any leads appreciated- JAX is the natural one, but their amplified sequences
> are
> PRE-mouse genome sequencing.
>
> > Date: Wed, 8 Jun 2011 16:17:12 -0700
> > From: [email protected]
> > To: [email protected]
> > CC: [email protected]
> > Subject: Re: [Genome] mouse microsatellite DMIT amplified sequences
> >
> > Hello Ann,
> >
> > We don't have URLs to specific sets or subsets of data, so I'm not sure
> > I can help you. You might try going to MGI directly:
> > http://www.informatics.jax.org/ and searching for the data there.
> >
> > --
> > Brooke Rhead
> > UCSC Genome Bioinformatics Group
> >
> >
> > On 06/05/11 16:01, ann eileen miller baker wrote:
> > > 5Je11
> > > May I be sent the URL to access mouse DMIT amplified sequences?
> > > In early drafts, the file with amplified sequences also included
> > > (1) DMIT primer sequences
> > > (2) DMIT alleles of mouse inbred strains
> > > If those are on the same or another URL, please send that URL too.
> > > Thanks.
> > >
> > > _______________________________________________
> > > Genome maillist - [email protected]
> > > https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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