Aligned NBRF/PIR Format

Multalign Viewer displays sequence alignments and single sequences.

Sequence alignments can be read/written in aligned NBRF/PIR format, a simple variant of standard NBRF/PIR format. In an aligned NBRF/PIR file, all of the sequences are made the same length by including characters for leading, trailing, and gap positions. Multalign Viewer tolerates any non-alphanumeric characters except asterisk (*) in these positions. In rhod.pir, for example, dashes (-) are used. The second line for each sequence is required, but may be blank; if it is omitted, the first line of sequence will be interpreted as comments and left out of the sequence. Spaces within sequences are ignored.

Single sequences can be read/written in standard NBRF/PIR format, but a file that contains multiple unaligned sequences (sequences of different lengths) will not be accepted.

UCSF Computer Graphics Laboratory / November 2009