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
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