RSS Feed PROFILE-SS
PROFILE-SS is a program that combines the optimal local sequence alignment algorithm developed by Michael Watterman and Mark Eggert and the profile analysis methods of Gribskov into one program that finds the N-best alignments between a database sequence and a profile.
Installed on: the Opteron Cluster.
The first step in the profile analysis process is to locate a number of related sequences. This is done by using another sequence analysis program, like MAXSEGS, to search a database with a single sequence.
Once a few related sequences are located, programs like the GCG PILEUP program, the MSA program, and others are used to construct a multiple sequence alignment. This multiple sequence alignment should then be placed in the GCG MSF file format.
The multiple sequence alignment (in the MSF format) is then fed into the GCG PROFILEMAKE program, which creates a profile that can be used in conjunction with the PROFILE-SS program to probe the databases for all related sequences.
Opteron v. 1.9
PROFILE-SS users will find it convenient to use the /biomed/lib/examples/.login.fixed login file. It adds to your default path directories where many sequence analysis packages are stored, sets up the environment for EMBOSS, and defines some environment variables for sequence analysis packages.
Usage:
/biomed/bin/profiless
Other PROFILE-SS documentation:
- Sequence analysis tutorials developed at PSC.
- PROFILE-SS version 1.8 User Manual.
- PROFILE-SS version 1.7 User Manual.
- For detailed information on the Watterman and Eggert sequence alignment algorithm and its extensions refer to The Journal of Molecular Biology(1987) 197, pp 723-728.
- For information about Gribskov's profile analysis method, refer to Methods in Enzymology (1990) 183, pp 146-159.
See also:
- Other nucleic acid and protein sequence analysis packages installed at the PSC.