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README.txt 2012-11-29 1.6 kB
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SSEA.java 2012-11-29 12.1 kB
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The SSEA is written by Ren-Xiang Yan in Ziding Zhang's laboratory.
License: Anybody can use this code for any purpose, including
teaching, research, and commercial purposes, provided proper
reference is made to its origin. 
Any questions can contact Ren-Xiang Yan in China Agricultural University. Email:simpleyrx@163.com


Usage:  java -jar  SSEA_target_DB.jar target_ssea ssea_DB output_file view_align

Example: java -jar ssea_target_DB.jar seq.ss ssea_db.fasta ssea_out false    # This commnad only return the ssea scores.
         java -jar ssea_target_DB.jar seq.ss ssea_db.fasta ssea_out true     # This commnad return the ssea scores with alignments.
         

Note: 
1.Users should use java 1.5 or newer version.
2.Fomrat: Every sequences's secondary structure have two lines. The first line is the annotation information.
	  The second line is secondary structure.
	  
3. "H" represents a helix element, "E" denotes a strand element, and "C" stands for a coil element. The two secondary structure elements were aligned using a dynamic programming algorithm. 
In shorten mode 
The secondary structural element strings were shortened and the length of each element was retained for the scoring of SSEA. For example, the secondary structure string HHHHCCCCCEEEEEHHHH would have been shortened to HCEH and the lengths of each element (i.e., 4, 5, 5, and 4) were stored. Then the scoring function for SSEA is adopted from Przytycka et al (1999). 
In extension mode 
In extension mode, the alignment were extended based on the shorten mode and protein residues. 
	  
	
     
Source: README.txt, updated 2012-11-29