IGLOSS: iterative gapless local similarity search
Explanation of the method can be found at: http://compbioserv.math.hr/igloss/
Program takes four arguments:
proteome_file_name
query_file_name
scale
number_of_iterations
Proteome file can be in fasta or text format.
Query file consists of one or more rows of amino acids symbols ARNDCQEGHILKMFPSTWYV.
Symbols 'X' and 'x' standing for any amino acid symbol are allowed.
One extra row of 0 and 1 is allowed, where 1 stands for a conserved position.
All rows in the query file must be of equal length.
Scale is a positive float. This parameter measures similarity between the input query and the response. The higher it is - higher is the similarity. Reasonable scale is from 3 to 15.
Number of iterations is selfexplanitory.
IGLOSS.cpp calls logistic.py to make a logistic fit of the data.
IGLOSSnopy.cpp is IGLOSS.cpp without calling logistic.py for logistic fit. It makes an estimation of logistic fit via mean and standard deviation of the data.