"The string between the asterix is the order in which amino acids are to be considered (\' \' denotes gap). The matrix of rows 1-10 contains 1s and 0s corresponding to whether each amino acid has a particular property. For example, Cysteine has the properties \'Hydrophobic\' and \'Small\'. It also has the \'anti-properties\' \'not-Polar\',\'not-Proline\', \'not-Positive\', etc.",
],
"maxalig"=> [
"This specifies the number of sub-alignments to be considered when calculating %C. If the possible number of sub-alignments (of the size specified with -s <N>) is less than or equal to this value, then all possible sub-alignments will be generated and considered for the calculation of %C. If the number of possible sub-alignments is greater than this number, than a random sample of alignments (i.e., this number) will be generated.",
],
"minprop"=> [
"This is the minimum number of properties to be shared at all positions within a sub-alignment to define a position as conserved. If you don\'t understand this, see the above paper, and references therein.",
],
"window"=> [
"It is sometimes desirable to consider only *runs* of conserved positions within an alignment (ie. runs of 3 or more). -w specifies the minimum run of conserved positions to be allowed. The default is 1 (ie. all conserved positions are used)",
],
"ignseq"=> [
"Errors in sequencing, and other problems sometimes make it desirable to ignore a certain fraction of residues. -f allows a user defined fraction of amino acids to be ignore in the calculation of %C. The default is 0. (ie. no amino acids are ignored)",
],
"mingap"=> [
"It is sometimes desirable to allow for gaps at conserved positions because of missing sequences, etc. This specifies the number of gaps tolerated at a position during the definition of conservation. The default is 0. (ie. no gaps are allowed)",
],
"seqomit"=> [
"Sometimes it is necessary to ignore particular sequences in the alignment. This option allows the user to specify sequences to be ignored by simply typing in their position in the block file (ie. all sequences considered to be numbered starting at 1). By default, no sequences are ignored, except for those sequences having identifiers ending in \'dssp\', \'define\', \'rk\', or \'str\', these being standard names for secondary structure strings (often showed beside alignments). Identifiers called \'space\' are also ignored.",
],
};
$self->{SCALEMIN} = {
};
$self->{SCALEMAX} = {
};
$self->{SCALEINC} = {
};
$self->{INFO} = {
};
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/assp.pm
$self->_init_params(@params);
return$self;
}
1; # Needed to keep compiler happy
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