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Unformatted text preview: CMSC 423: Project #1: Multiple Sequence Aligner Due: Tuesday, November 15th at 11:59pm. You will build a multiple sequence aligner. Youll implement the 2-approximation to MSA using a ffi ne gaps. Your program must be written in Java. You should work in groups of 2. Part of your grade for the project will be based on a confidential survey completed by your partner. Your program will perform alignment using an a ffi ne gap scoring system with parameters read from a scoring matrix file and a multi-FASTA file (format given below) and output the 2-approximation to the MSA under the sum-of-pairs score also as a multi-FASTA file with gaps inserted. Format of the command: Your program will be run using the following command: java msa.jar score.matrix in.fasta out.fasta Your program must run and compile on the submit server. Format of the multi-FASTA file: The multi-FASTA file contains any number of sequences. A sequence begins with a line containing a > character in the first column. Following the > on the same line there is name for the sequence. This name ends at the first space or at the end of the line whichever comes first....
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.
- Fall '07