DEGSITE compares a nucleotide sequence to a collection of labeled motif sequences and identifies those sites in the nucleotide sequence where an inexact match to the motif is found. The upper limit of non-matches permitted is explicitly chosen by a user: 1 or 2. The program produces three possible outputs. The first is a screen display of the position and the motif label in ascending order of position for successful matches. The second is an ASCII text file in the style of the output of the MAP algorithm in the GCG suite with each section being 50 positions wide. The third is an ASCII text file with a list of positions, in ascending order, provided in front of material identical to the second option.

Upon starting DEGSITE, the user must provide, in response to programmed query, the user-determined parameters:
	a) the number of non-matching positions allowed for a successful comparison,
	b) the output desired,
	c) the name of the file containing the collection of labeled sequence motifs,
	d) the name of the file containing the nucleotide to be examined and, if necessary,
	e) the name of the output file - the default file name is the name of the nucleotide sequence file.

The two input files must be in the same directory as the executable code. The file of the collection of labeled sequence motifs must have the extension ".mtf". The contents of the file is a series of lines with the contents of each line being the motif label followed by any punctuation character followed by the motif sequence. The motif label may be a string of any alphanumeric characters up to 15 characters in length. The motif sequence may be up to 20 nucleotides in length. The comparison is case-insensitive, thus removing this potential constraint upon the contents of the two files.

The program is intended for focused use rather than general use. 100 is the maximum number of positions in the sequence under examination where an inexact match can be found. The maximum number of inexact matches at any particular position is 10. These boundaries are inherent to the source code. For the comparison algorithm there is no code-based limit upon the length of the nucleotide sequence in the ".seq" file. Likewise for the output provided the 100X10 boundary is not exceeded. However the part of the output which indicates position will cease providing appropriately incrementing integers at 2000 bp. There is no code-based limit upon the number of motifs contained in the ".mtf" file.

Ambiguity in the motif sequence and the nucleotide sequence under examination are accomodated for the case when any nucleotide can be present at a position. When this occurs in either solely the the motif or both, it is always considered a match since either situation will result in a match with the motif sequence whatever is present in the examined sequence. When this occurs only in the examined sequence it is always considered a mismatch.