Complete Homology-Assisted Ms/ms Protein Sequencing(Champs)
Champs is a tool for automatic protein sequence assembly.
To run Champs, Sun's Java Running
Environment (JRE) 6.0 is required. If JRE is not installed, please go to
to download and install the JRE.
There are two input files. The first input file contains a reference
The Second input file contains the alignment output of SPIDER.
Each alignment have five lines: digestion enzyme, de novo tag, spider tag, reference tag and similarity score
Run Champs with four arguments:
(1) reference protein file name (2) alignment file name (3) alpha (4) result file name.
Alpha is a real number argument discussed in the paper.
We will illustrate the usage of Champs by an example.
Suppose the reference protein file name is "ref.txt", the alignment file name is "align.txt", alpha = 7.0, use the following line to run Champs.
java -Xmx1024m -jar Champs.jar ref.txt align.txt 7.0 result.html
The output file (result.html in the above example) contains the predicted protein sequence and the confidence score for each residue (Example result.html).