Search sequence documentation. Slow, use SRS and Entrez! emboss textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html $html_out1 -auto Sequence Pattern to search for Do a case-sensitive search No Yes Display column headings Yes No Display the USA of the sequence Yes No Display accession column Yes No Display name column Yes No Display description column Yes No Format output as an HTML table No Yes You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html