======================== HyPep DESCRIPTION ======================== A hybrid peptide sequencing method with the combination of regional sequence alignment and homology database search is developed to improve the peptide identification. ================ Download HyPep ================ HyPep (ver 1.0) is a Java executable application and supports most operation systems. It can be freely downloaded from http://pages.cs.wisc.edu/~yadi/bioinfo/hypep/hypep.html It is for research use only, permission is required for comercial use. ============================ Install and configure HyPep ============================ Unzip HyPep.zip and place the resulting HyPep folder in any location. In the folder, lib cannot be modified or deleted. Sample input.txt and Fasta_PepDB.txt are also included for test. ================== How to run HyPep ================== To run HyPep, user needs to: 1) select an input file which only contains peptide sequences, each sequence per line. 2) specify a FASTA formatted database file. 3) Choose an output file which has already been created by user. There are two parameteres for use to set: 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]. click "Run". The running information can be seen in the monitor window. ==================== Author and Copyright ==================== Author: Weifeng Cao, Yadi Ma Contact: wcao2@wisc.edu Copyright belongs to Li lab at University of Wisconsin-Madison. April 07, 2011.