Extract sequences by name from a sequence list

To extract sequences by a single name from a sequence list, use the Find function (Edit -> Find in Document) to find the name of your sequence. The In Sequence Names option will need to be selected, and you can select Find Next to find the first matching result, or Find All to find all documents that match your search term.


To then extract your sequence(s) from the list, select Close to exit the search window. This will leave your search results selected in the sequence viewer. You can then extract the sequence from the sequence list by selecting the Extract button above the sequence viewer. If you have multiple search results this will extract all of those results to a separate sequence list, otherwise your single sequence will be extracted.


To extract sequences by multiple names from a sequence list, you can repeat this process for each sequence name or use the Extract Sequences by Name workflow available in Geneious R8 onwards that will allow you to specify multiple names at once. This workflow can be run from the Workflows -> Run Workflow menu by selecting Extract Sequences by Name in the dropdown box.


Enter the names you want to search for, separated by your chosen separator.  If Match partial names is selected, Geneious will extract sequences where only part of the sequence name matches the query. The Extract partial name matches to separate documents setting will extract any partial matches to a separate sequence list to the exact matches. You can also perform an inverse extraction, where only the names that do not match your search term are extracted by specifying the Extract inverse instead option.


Geneious will automatically extract any sequences that match your search results to a new file with the name filtered <document_name>.



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