|FASTA format: A sequence record in a
FASTA format consists of a single-line description (sequence name), followed by
line(s) of sequence data. The first character of the description line is a greater-than (">") symbol.
FASTA format Example:
Any non-alphabetical character in the input sequences is ignored by MUMMALS. The letters ([BJOUXZbjouxz]) that do not belong to abbreviations of the twenty standard amino acids are treated as alanines in alignment process, but are unchanged in the final alignment.
The number of sequences in the input data is determined by the number of lines beginning with a ">". If only one line begins with a ">", the program gives an error message. If there are no lines beginning with a ">" in the input data, a warning message will appear and the input file is assumed to be in a CLUSTAL format, in which each sequence and its name are on the same line and the sequences can be partitioned into a number of blocks separated by empty lines. The word "CLUSTAL" indicating the format can begin in the first line, but such a first line is optional.
CLUSTAL format Example:
The output alignment of MUMMALS is in CLUSTAL format.