423prj2 - CMSC 423: Project #2: Finding Several Good Local...

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: CMSC 423: Project #2: Finding Several Good Local Alignments Due: Tuesday, December 8th at 11:59pm. In this second project, you will implement local alignment with a ffi ne gaps along with a scheme for finding several good alignments, not just the best. The project will be done in groups of 2 these groups can be di erent from those in part 1. Some of your grade for the project will be based on a confidential survey completed by your partner. Format of the command: Your program will be run using the following command: java multilocal.jar score.matrix in.fasta out.fasta k where k is an integer that gives the desired number of alignments. Your program must compile on the submit server. It should output into out.fasta the k best local alignments of the two sequences in in.fasta (see below). Format of input: The format of the score.matrix file will be the same as in Project #1. The format of the in.fasta file is the same as in Project #1 as well, except that it can contain only 2 sequences. Youfile is the same as in Project #1 as well, except that it can contain only 2 sequences....
View Full Document

Ask a homework question - tutors are online