May 2007
GFS Version 2
05/23/07 19:28 Filed in: Work
We have now officially completed GFS Version 2. What
is GFS version 2? Based upon the original
Genome-based Fingerprint Scanning program, GFS V2 is
designed as a general-purpose, open proteomics search
engine. Its specialty is matching mass spectrometry
data (both MS and/or MS/MS in V2!) to
unannotated genome sequences. In other words, if you
want to perform a proteomic search against an
unannotated genome, or you don't fully trust the
computational gene predictions in the database, GFS
might be for you. You can try it at our redesigned
website http://gfs.unc.edu, or
just drop us a line and we'll send you a link
for downloading the full set of source and
executables from ProteomeCommons (under a liberal
Apache-style license). We will publicize the
link as soon as we have our manuscript detailing
version 2.0 out the door.
New Features in Version 2.0
• Runs on multiple platforms! Specifically, we provide pre-compiled binaries for Windows, Linux, and Mac OS X
• MS/MS data - GFS now has two modes to take advantage of tandem MS data, both a "shotgun" mode and a Peptide Mass Fingerprint mode.
• Distributed/Cluster usage - GFS has a built-in system for distributing searches over a compute cluster
• Post Translational Modifications (PTMs) - GFS V2 now has support for PTM's (only for PMF mode at present)
• Many speed & Memory improvements and bug fixes
• Gene-scanning mode - use annotations if you have them. This may be particularly useful for comparing results between matches to annotated genes versus raw genome
• Batch mode - run many files at once
For more details on what is in version 2.0, feel free to have a look at our draft manual (which is a work in progress).
Coming soon, Version 2.1!
We are hard at work on version 2.1 already, which is planned for a November 2007 release. Version 2.1 will include:
• A new very high accuracy MS/MS matching mode, that does a much better job for matching shotgun results against large genomes
• A newer cluster/distributed computing implementation, allowing a search to be divvied up into 100's or even 1000's of jobs to take full advantage of available compute resources.
• Bug fixes for the B+ Tree mode.
• 64 bit operation
If you are interested in beta testing GFS with the above features, please drop us a line.
New Features in Version 2.0
• Runs on multiple platforms! Specifically, we provide pre-compiled binaries for Windows, Linux, and Mac OS X
• MS/MS data - GFS now has two modes to take advantage of tandem MS data, both a "shotgun" mode and a Peptide Mass Fingerprint mode.
• Distributed/Cluster usage - GFS has a built-in system for distributing searches over a compute cluster
• Post Translational Modifications (PTMs) - GFS V2 now has support for PTM's (only for PMF mode at present)
• Many speed & Memory improvements and bug fixes
• Gene-scanning mode - use annotations if you have them. This may be particularly useful for comparing results between matches to annotated genes versus raw genome
• Batch mode - run many files at once
For more details on what is in version 2.0, feel free to have a look at our draft manual (which is a work in progress).
Coming soon, Version 2.1!
We are hard at work on version 2.1 already, which is planned for a November 2007 release. Version 2.1 will include:
• A new very high accuracy MS/MS matching mode, that does a much better job for matching shotgun results against large genomes
• A newer cluster/distributed computing implementation, allowing a search to be divvied up into 100's or even 1000's of jobs to take full advantage of available compute resources.
• Bug fixes for the B+ Tree mode.
• 64 bit operation
If you are interested in beta testing GFS with the above features, please drop us a line.
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