This is an old post, but for the benefit of future googlers: a sed 's/*//g' solution is absolutely safe in terms of escaping (I would not do it with the -i option though) - there is no reason for panic. tr -d '*' would be more elegant though. BUT: nothing can replace a format-aware utility, because in a general case stops can appear not only in the end of a protein sequence but also in the middle (which is not expected for Transdecoder though), and asterisks are allowed to appear in headers. The golden standard is emboss's transeq which has the -trim and -clean options to strip the final or all stops respectively.