The SAF is a facility in the Biology Division at Caltech. It
provides researchers with computing resources for use in their
investigations of a variety of biological problems. It is also used in the
teaching of several undergraduate courses. For historical and
political reasons the SAF is divided into two entitities: the sequence
analysis facility and the structure analysis facility.
The sequence analysis facility provides a variety of tools and data for use
primarily by molecular biologists. A typical set of tasks that a
researcher might perform would be:
The structure analysis facility provides a complementary set of tools and
data primarily for use by structural biologists. A typical set of tasks
that the same researcher might perform would be:
- 1. Assemble the many sequence fragments from a DNA sequencing project
into one final DNA sequence
- 2. Take that sequence and search the DNA and Protein databases for entries
that are similar to it.
- 3. Perform a multiple sequence alignment on the set of similar
protein sequences thus found.
- 4. Perform a phylogenetic analysis on the aligned set of similar
Sequence analysis often leads to structure analysis and
vice versa. The SAF provides a place to do both.
The sequence analysis work is carried out on a Solaris 2.8 workstation.
Data from the DNA sequencing facility
is also served from this machine.
The structure analysis work is performed on one of
seven workstations which dual boot linux and Windows XP,
all of which are equipped with Stereo hardware.
- 5. Examine the known structure of one of the similar proteins and
extrapolate from that a probable structure for the new protein that is the
focus of the research.
- 6. Modify an existing protein model by substituting amino acids at
various points in the chain and predict from that those substitutions most
likely to affect the properties of the protein.
- 7. Attempt to model the docking of two proteins,
or one protein and a ligand, when the structures of each are known and the
pair are known to interact.