Hi again Horia, I'm sorry, I told you to select the wrong table. In fact, you need to select a table from the Genes and Gene Predictions track group. Then the CDS FASTA option should show up in the output format drop-down menu. After hitting "submit", you will see a page that allows you to select from different mutliz alignments.
Sorry for the confusion, and please let us know if you have any further questions! -- Brooke Rhead UCSC Genome Bioinformatics Group On 02/03/09 04:02, Stanescu, Horia (NIH/NHGRI) [F] wrote: > Hello Brooke, > and thank you for your answer. For some reason though I still can't > get to the CDS FASTA option under the output format drop-down menu in the table browser. > Please see the attached screen capture - maybe you get an ideea of what I might be doing wrong. Sorry to bother you again, > Horia > > > > -----Original Message----- > From: Brooke Rhead [mailto:[email protected]] > Sent: Mon 02/02/2009 15:35 > To: Stanescu, Horia (NIH/NHGRI) [F] > Cc: [email protected] > Subject: Re: [Genome] how to download translated sequences from conservation > group > > Hello Horia, > > There is new functionality in the Table Browser that will do this. > Choose "output format: CDS FASTA alignment from multiple alignment". To > see the option in the drop-down menu in the Table Browser, choose > "track: Conservation" and "table: multiz44way". (The 44-way > conservation track was released last week and is called "Conservation". > The old 28-way track is now called "28-way Cons".) > > There are some options to choose from after hitting "submit", explained > in the User's Guide: > > http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA > > The tool can also be accessed from the details pages of several gene and > gene prediction tracks, such as UCSC Genes and RefSeq Genes. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 01/31/09 14:32, Stanescu, Horia (NIH/NHGRI) [F] wrote: >> Hello, >> can you please tell me how one could get a file with the amino acid > sequences for a given gene for all the species that are visible in the > genome browser at the comparative genomics track when the codon > translation is checked as: 'Use default species reading frames for > translation'? >> I have tried the table browser (group: comparative genomics, track > 28wayCons - btw isn't 44wayCons available yet? - but the table structure > is somewhat opaque for my understanding, sorry! >> Thank you very much, >> Horia Stanescu >> >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome > > > ------------------------------------------------------------------------ > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
