We investigate a problem from computational biology: Given a constant size alphabet M with a weight function / : M--> +, find an efficient data structure and query algorithm solving the following problem: For a weight M C + and a string cr over A, decide whether cr contains a substring with weight M (ONE STRING MASS FINDING PROBLEM). If the answer is yes, then we may in addition require a witness, i.e. indices i _ i and ending at position j has weight M. We allow preprocessing of the string, and measure efficiency in two parameters: storage space required for the preprocessed data, and running time of the query algorithm for given M. We are interested in data structures and algorithms requiring subquadratic storage space and sublinear query time, where we measure the input size as the length of the input string. We present two efficient algorithms: LOOKUP solves the problem with O(,) space and (Wg ' loglog,) time; INTERVAL solves the problem for binary alphabets with O0, ) space in O(log,) time. We sketch a third al-gorithm, CLUSTER, which can be adjusted for a space time tradeoff but for which we do not yet have a resource analysis. We introduce a function on weighted strings which is closely related to the analysis of algorithms for the ONE STRING MASS FINDING PROBLEM: The number of different submasses of a weighted string. We present several properties of this function, including upper and lower bounds. Finally, we introduce two more general variants of the problem and sketch how algorithms may be extended for these variants.

biollogical samplle, provides many challlenges in data reprresentation, inteegration, and interpretation. In this article, we survvey experimenntal and compuutational approoaches related to protteomics, focusiing on the waays in which recent biologiical finddings complicatte the mapping from genes to RNA to proteein. We argue that the challenges encoountered in prooteomics providde a valuuable lesson on the complexity of life itself, as live organissms alwaays contradict oversimplified models of bioloogical informatiion floww. It is an exciiting new field

Mechanisms by which TFG functions in protein secretion and oncogenesis

To identify key regulators of subminimum inhibitory concentration (sub-MIC) antibiotic response in the Pasteurella multocida proteome, we applied systems approaches. Using 2D-LC-ESI-MS 2, we achieved 53 % proteome coverage. To study the differential protein expression in response to sub-MIC antibiotics in the context of protein interaction networks, we inferred P. multocida Pm70 protein interaction network from orthologous proteins. We then overlaid the differential protein expression data onto the P. multocida protein interaction network to study the bacterial response. We identified proteins that could enhance antimicrobial activity. Overall compensatory response to antibiotics was characterized by altered expression of proteins involved in purine metabolism, stress response, and cell envelope permeability. Copyright © 2008 Bindu Nanduri et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1.

Software UniPep- a database for human N-linked glycosites: a resource for biomarker discovery