A hybrid peptide sequencing method with a combination of regional sequence alignment and homology database search is developed to improve peptide identification.


To run HyPep, a user needs to:
1) Select an input file which contains peptide sequences, one sequence per line: (Example)
2) Specify a FASTA formatted database file: (Example)
3) Choose an existing output file (if the file is not empty, its content will be overwritten after running HyPep). After running HyPep using input and database examples above, the output file will look like this.

A user can customize two parameteres: sliding window size and score threshold.
Sliding window size defines the regions in database seuqence to align the amino acid in query sequence. The default value is 3.
Score threshold is used to cut off low-score alignment. The default value is 1.00. The range for score threshold is [0, 4.00].

Run HyPep

Download HyPep from here. Please read me before running HyPep.
Last modified: April 07, 2011