DCSE, AN INTERACTIVE TOOL FOR SEQUENCE ALIGNMENT AND SECONDARY STRUCTURE RESEARCH

DCSE provides a user-friendly package for the creation and editing of sequence alignments. The program runs on different platforms, includin g microcomputers and workstations. Apart from available hardware, the program is not limited in the size of the alignment it can handle. It deviates more from classical text editors than other available sequenc e editors because it uses a different approach towards editing. It shi fts characters or entire blocks of aligned characters, rather than ins erting or deleting gaps in the sequences. Alignment of a new sequence to an existing alignment is partly automated. Although DCSE can be use d on protein sequence alignments, it is especially targeted at the exa mination of RNA. The secondary structure for every sequence can be inc orporated easily in the alignment. DCSE also has extensive built-in su pport for finding and checking secondary structure elements. A sophist icated system of markers allows notation of special positions in an al ignment This system can be used to stare information such as the posit ion of hidden breaks, introns and tertiary structure interactions.