The UCSD Jacobs School computer scientists designed algorithms that literally pick up the pieces from here. The algorithms glue the overlapping pieces together until they have reassembled a series of possible original ring structures, explains Julio Ng, a graduate student in UCSDs Interdisciplinary Bioinformatics Ph.D. program and RECOMB 2008 paper co-author.
The algorithms make use of data on the weights of the various NRP ring fragments collected at each stage using mass spectrometry. This work is an extension of an award-winning automated approach Bandeira and colleagues used to reconstruct snake venom peptides.
Our Recomb 2008 paper represents the first demonstration of de novo sequencing of nonribosomal peptides. Without knowing the structure of the original compound, we can determine it, explains computer science professor Pavel Pevzner, the last author on the RECOMB 2008 paper and the director of UCSDs Center for Algorithmic and Systems Biology which is part of the UCSD Division of the California Institute for Telecommunications and Information Technology (Calit2).
In their RECOMB 2008 paper, the researchers document how they used de novo sequencing to determine the structure of two different nonribosomal peptides. In order to be able to verify their results, the researchers chose peptides that had been independently sequenced using a slow, labor intensive, costly and somewhat inconsistent nuclear magnetic resonance (NMR) approach. NMR provides information on the position of specific atoms within a molecule by using the magnetic properties of nuclei. The team is now working on more than ten additional compounds and has filed a provisional patent for the technique.
This project arose after Roger Linington from UC Santa Cruz, a co-author on the RECOMB 2008 paper, approached Dorrest
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University of California - San Diego