Sequence concatenation

Sequence expressions can be concatenated with the + operator. Concatenation links together corresponding pairs in the left and right sequence sets. Following are some rules concerning sequence concatenation:

• When one of the sets is a singleton (for example, a literal), concatenation results in prepending or appending that single sequence to every sequence in the other set.

• If a concatenation includes more than one fragment from the same source sequence, then feature reassembly occurs when writing to a file format supporting features. Feature reassembly takes parts of the same feature in multiple fragments and combines them back into a single feature. When features are cut, reassembled, or (in some cases) offset, SeqNinja flags this with an annotation of the form: /note=”***needs review***Explanation, where Explanation is a short description of a potential issue (e.g., that the head or tail of a feature has been cut by a number of residues).

• A sub-sequence can cut a feature. Multiple sub-sequences concatenated together can temporarily result in multiple fragments of the same feature. SeqNinja can reassemble these fragments so that the output sequence has a single feature, and such fragments are reassembled if they do not overlap. Reassembly is performed left-to-right in the resulting sequence. For example, the “source” annotation in GenBank files can be cut into fragments by a SeqNinja expression. Before writing an output file, SeqNinja reassembles these fragments, as long as they don’t overlap. If a concatenation does not include multiple fragments from the same source, feature reassembly does not occur.