Enhanced FASTA format

The enhanced FASTA format is the same format as FASTA format except that gap penalty arrays can be appended below the sequence. Gap penalties are enclosed in curly brackets {}. The gap open array, gap extension array and terminal gap extension array are recognized by the tags 'gpo:', 'gpe:' and 'tgpe:' respectively. If there is a leading char '#' within the brackets {}, this gap penalty array is commented out. Gap penalties can be supplied in the following two formats, but can not be mixed in the same input file.

  1. An array of real values enclosed in {} and delimited by white spaces. e.g. {gpo: 1 1 1.5 1.5 1.5 0.5 0.5}. In this case, the number of real values should be exactly the same as the number of residues in the sequence.
  2. Index:value, e.g. 1-15:2.0 means the residues 1 to 15 are assigned with value 2.0. For unassigned residues, the default value is 1.

The value of each element is not the absolute gap penalty but the scale of the default gap penalty for KalignP, e.g. {gpo: 1:2.0} means that the gap open penalty of the first residue will be set to 2.0*10, if the default gap open penalty is 10. We use the scale instead of the absolute gap penalty since it is easier to understand how position specific gap penalty varies. Moreover, it avoids possible conflicts when the general gap penalty is reset by the ``-gpo'', ``-gpe'' or ``-tgpe'' option of KalignP. An example is shown below in both formats. The sequence is ASNLSKLFLSDSDA. All three types of gap penalty arrays are supplied, but gap extension array and terminal gap penalty array are commented out by the leading char `#' and thus only the gap open array is effective.

Example in format 1:

Note that the size of the array should be exactly the same as the length of the sequence. 

>seq1
ASNLSKLFLSDSDA
{gpo: 1.5 1.5 1.5 1.5 1.5 0.5 0.5 0.5 0.5 0.5 1 1 1 1}
{#gpe: 2 2 2 2 2 0.4 0.4 0.4 0.4 0.4 1 1 1 1}
{#tgpe: 2 2 2 2 2 2 2 2 2 2 1 1 1 1 }

Example in format 2:

>seq1
ASNLSKLFLSDSDA
{gpo: 1-5:1.5 6-10:0.5}
{#gpe: 1-5:2.0 6-10:0.4}
{#tgpe: 1-10:2.0}