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Project Files (on the "student" server).

You may copy the following files into your student account:
Assignment 1:

  • /u/staff/biol/vprobon/sufIsEscherichiaShigella (a collection of coding sequences of sufI homologs from Escherichia and Shigella species/strains)
  • /u/staff/biol/vprobon/sortscale (This is a tRNA abundance scale for E. coli. An approximation of translation speed for each codon can be computed by the inverse of these values)
  • /u/staff/biol/vprobon/CLUSTALW/clustalw-2.1-linux-x86_64-libcppstatic/clustalw2 (clustalw version 2, Linux 64bit executable).

Also in the folder /u/staff/biol/vprobon/CLUSTALW/clustalw-2.1-linux-x86_64-libcppstatic/ you may find the clustalw2 help file, and example files for testing the software.
Assignment 2:

  • /u/staff/biol/vprobon/CAST/CASTSERIAL (CAST: C++ serial implementation)
  • /u/staff/biol/vprobon/CAST/UniRef50stats (UniRef50 statistics, by Stella Tamana)

For help on using CASTSERIAL enter on the command line ./CASTSERIAL -help
Use CASTSERIAL with the default parameters and the -stat switch, to produce a cast.stat file.
Assignment 3:
Hydrophobicity scale: Use one from those available at http://blanco.biomol.uci.edu/hydrophobicity_scales.html
Helix-forming potential: Use the one reported in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299714/?tool=pmcentrez
Assignment 4:
Genetic codes available in: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi 
Assignment 5:
Assignment 6:

  • /u/staff/biol/vprobon/CAST/CASTSERIAL (CAST: C++ serial implementation)
  • /u/staff/biol/vprobon/CAST/CASTMULTI (CAST: C++ multithreaded implementation)
  • /u/staff/biol/vprobon/SEG/seg (SEG: original C implementation)
  • /u/staff/biol/vprobon/SEG/seg.doc (SEG documentation in plain ASCII text)

For help on using CASTSERIAL enter on the command line ./CASTSERIAL -help
For help on using CASTMULTI enter on the command line ./CASTMULTI -help
For help on using SEG enter on the command line ./seg or consult the seg.doc file
You should use CAST (serial and multi-threaded version) and SEG with their default parameters.
Use CASTSERIAL/CASTMULTI with the  -stat switch, to produce a cast.stat file. Keep a copy of  cast.stat before the next run, or the file wil be overwritten.
In order to benchmark performance rely on the system command time. Thus, you should invoke each program on the command line, preceeded by the time command, which reports a rough estimate of the time needed for your program to finish. 
Assignment 7:

by Dr. Radut.