Computational Biology Capstone: Project Software

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Note on Instructional Project machines as servers The machines at your disposal for capstone computing are the Instructional Project machines amlia, kiska, and umnak. These are distinct from the Instructional Lab Linux machines, which should not be treated like servers. If you need to work from a Windows machine or from home, log in to one of the Instructional Project (as opposed to Instructional Lab Linux) machines listed above to do your work. You can do your work in the directory /projects/instr/09sp/cse428. This space is not subject to the quotas imposed on student home directories. Subdirectories named a, e, and w have been set up for the three project teams and associated with unix permission groups cse428a, cse428e, and cse428w, respectively. Each student has been added as a member of his or her team's unix group. Mauve Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. A linux version of Mauve is available in the directory /cse/courses/cse428/09sp/mauve_2.2.0. Windows and Mac versions are also available for downloading from Mauve's home. Use Progressive Mauve, as this results in more accurate results. There is a newer "developer's snapshot" version of Mauve in the directory /cse/courses/cse428/09sp/mauve_snapshot. According to Mauve's developer: "There's an unfortunate bug in the 2.2.0 release that causes the GUI to fail in loading some genome alignments... The main new features not present in 2.2.0 [but presumably present in the snapshot] are contig reordering for incomplete genomes and tools to export lists of annotated gene orthologs, SNPs, and genome arrangements." Snapshots for other platforms are available. Genomes to input to Mauve are available at NCBI's Microbial FTP directory. You want to input the genbank (.gbk) files to Mauve, because this turns on some useful Mauve features. A sample Mauve alignment of 4 Streptococcus genomes that you can use as input to the Mauve visualization tool is available in a zip file. BLAST BLAST is available in the directory /cse/courses/cse428/09sp/blast. Add /cse/courses/cse428/09sp/blast/blast-2.2.19/bin to your $PATH variable to execute BLAST commands outside its directory.

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