GFS

Genome-based Fingerprint Scanning

Genome-based fingerprint scanning (GFS) is a program developed by the Giddings lab that maps peptide mass fingerprint data directly to raw genomic sequence, enabling rapid, low-cost identification of proteins in genomes for which annotation is lacking. An experimentally obtained peptide mass fingerprint is entered into the program, which then scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprint is derived. The software first generates a theoretical mass list by translating the genome of interest in 6 reading frames (3 each on the forward and reverse strands) and digesting the resulting proteins in silico according to cleavage rules associated with the specified protease (trypsin in this case). The algorithm then finds matches (within a given mass tolerance) between these theoretical masses and the input experimental masses. These matches (or hits) are grouped into high-density regions on the genome that can be scored according to a number of criteria and ranked by statistical significance. These regions are derived by scanning across the genome with a fixed-sized window and then each window is scored according to criteria detailed in the original GFS publication. The subset of windows whose scores exceed a window score cutoff are then selected for an additional scan (subject to a separate extension score cutoff) that extends the start and stop position of the window into a larger region.(Adapted from the “GFSHelp” help page at the Giddings Laboratory Website)

The Upton lab developed this JAVA interface to GFS and is grateful to the Giddings lab for access to the software and their help. This version of GFS should only be used with viral genomes (or similar sized DNA sequences) at our website (It can be used with larger genomes at the Giddings Lab site).

GFS is also integrated into our VOCs and VGO tools. A viral genome in our database will be shown on the GFS interface by selecting a virus from a menu through one of these tools. When using GFS from VGO, the results are plotted on a graphical genome view.

 

 

Getting started

If you’re new to GFS, click on the launch button (on the right) and use the Quick Start Page to learn the basics (or if you’re like us…  just start clicking!).

The VBRC also provides additional help resources for GFS:

 

 

References

Giddings MC, Shah AA, Gesteland R and Moore B (2003)
Genome-based peptide fingerprint scanning. Proc Natl Acad Sci USA. 100:20-5

 

Troubleshooting

If your system does not launch Viral Orthologous Clusters, it is probably missing Java Runtime Environment 1.5. Please see Java Web Start Setup and Java Web Start Tips for help.

 

Submit a feature request

Is there a feature that you think this tool needs? Submit a wish.


 

Comments are closed.