Hello Wei, The best advice is to also download the primary table for the track and to use that and your own tools to order the sequences in your fasta file. (Coordinates are in the primary table).
Currently there is no option to re-order entries in a fasta files using the Table browser. Thank you, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/26/10 11:47 AM, Wei Xia wrote: > > Dear all, > I tried downloading proteins sequences encoded by zebrafish chr 8. And I got > all the proteins sequences starts with transcript name (like > ENSDART00000073440 starts with ENSDART) in one file in fasta format. > And these sequences are arranged in the order of the transcript name or > protein id or gene name but not their genome locations. > In other words, for example, ENSDART00000057590 and ENSDART00000034004 are > neighbor in zebrafish chr 8 but are not put together in the file I downloaded > above. > However if I download protein sequences through ensemble export application > in ncbi format the protein sequences I got are arranged in the order of their > genome location but there is a 5 mb size limit if download there. > Thanks very for the help. > Wei > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
