Exercise: transeq

Let's practice using command line flags again. The new ones here are -sbegin and -send. These allow you to specify a subregion of your sequence; in this case we will ask transeq to translate only the part of tembl:xlrhodop that we have identified as the coding region. You should remember -outseq from Chapter 2.

unix % transeq tembl:xlrhodop -sbegin 110 -send 1171 -outseq xlrhodop.pep
Translate nucleic acid sequences

unix % more xlrhodop.pep

>XLRHODOP+1 Xenopus laevis rhodopsin mRNA, complete cds.
MNGTEGPNFYVPMSNKTGVVRSPFDYPQYYLAEPWQYSALAAYMFLLILLGLPINFMTLF
VTIQHKKLRTPLNYILLNLVFANHFMVLCGFTVTMYTSMHGYFIFGQTGCYIEGFFATLG
GEVALWSLVVLAVERYMVVCKPMANFRFGENHAIMGVAFTWIMALSCAAPPLFGWSRYIP
EGMQCSCGVDYYTLKPEVNNESFVIYMFIVHFTIPLIVIFFCYGRLLCTVKEAAAQQQES
ATTQKAEKEVTRMVVIMVVFFLICWVPYAYVAFYIFTHQGSNFGPVFMTVPAFFAKSSAI
YNPVIYIVLNKQFRNCLITTLCCGKNPFGDEDGSSAATSKTEASSVSSSQVSPA

We saw earlier that the SwissProt entry for this protein has the identifier opsd_xenla; test your understanding of EMBOSS so far by using needle to compare your translated product with the database sequence. Compare your findings with the SwissProt entry using SRS.