Sequin editor

R. Camposano, "Structural Synthesis in the Yorktown Silicon Compiler, in C.H. Sequin, editor, VLSVS , VLSI Design of Digital Systems, pp. 61-72, Vancouver North-Holland, 1988. 

Sequin s viewers are all interactive, in that double-clicking on an existing item (shown as a GenBank flatfile paragraph or a line in the graphical display of features on a sequence) will launch an editor for that item (e.g., feature, descriptor, or sequence data). 

As a final step. Sequin displays an editor that allows all orgaiusm and somce modifiers on each sequence to be edited (or entered if the definition lines were not aimotated). On confirmation of the modifiers. Sequin finishes assemhling the record into the proper structure. 

Figure 4.1. Viewing a sequence record with Sequin. The sequence record viewer uses GenBank format, by default. In this example, a CDS feature has been clicked, as indicated by the bar next to its paragraph. Double-clicking on a paragraph will launch an editor for the feature, descriptor, or sequence that was selected. The viewer can be duplicated, and multiple viewers can show the same record in different formats.

The sequence editor built into Sequin automatically adjusts feature intervals as the sequence is edited. This is particularly important if one is extending an existing record by adding new 5 sequence. Prior to Sequin, this process entailed manually correcting the intervals on all biological features on the sequence or, more likely, redoing the entire submission from scratch. The sequence editor is used much like a text editor, with new sequence being pasted in or typed in at the position of a cursor. 

The concepts behind feature propagation and the sequence editor combine to provide a simple and automatic method for updating an existing sequence. The Update Sequence functions allow the user to enter an overlapping sequence or a replacement sequence. Sequin makes an alignment, merges the sequences if necessary, propagates features onto the new sequence in their new positions, and uses these to replace the old sequence and features. 

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