Hi Ann, We do not have tools for converting data from fasta format to Excel format. I looked back at one of your previous questions and I see that you mentioned you were able to use a tool from Oklahoma State to do this conversion. It may have been this tool: http://darwin.biochem.okstate.edu/fasta2tab/
Also, Galaxy (http://main.g2.bx.psu.edu/) has some data manipulation tools that should be of help. Go to their site, and on the left select "FASTA manipulation" and select "FASTA-to-Tabular converter". Please see our citation page page (http://genome.ucsc.edu/cite.html) for information on how to site the UCSC Genome Browser and the UCSC Table Browser: For citing the data used, you can see the "Credits" section in the STS Markers track description: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=stsMapMouseNew Please contact the mail list ([email protected]) again if you have further questions. Katrina Learned UCSC Genome Bioinformatics Group ann eileen miller baker wrote, On 6/9/2011 5:44 PM: > 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 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
