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
