Mathematical Approaches to Polymer Sequence Analysis and Related Problems

Abstract

), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights.Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) PrefaceMany problems arising in biological, chemical, and medical research, which could not be solved in the past due to their dimension and complexity, are nowadays tackled by means of automatic elaboration. Powerful computers are indeed used intensively for solving many problems having biological origin, thus creating the emerging field of science called "bioinformatics." However, the success of such approaches depends not only on brute computational strength of those computers, but also, and often critically, on the mathematical quality of the models and of the algorithms underlying those solution procedures.Solving a problem may be seen as converting information, in such a way that the solution of the problem (information in output) is extracted from its description (information in input), possibly passing through a number of intermediate states.By adopting this view, information handled when dealing with many of the abovementioned problems becomes, at some stage, a sequence. Nature often encodes relevant information into sequences. Therefore, a central role in bioinformatics is played by sequence analysis problems or by the related problems of analyzing the effects or the behavior of some sequence.The present volume offers a detailed overview of some of the most interesting mathematical approaches to sequence analysis and other sequence-related problems. Special emphasis is devoted to problems concerning the most relevant biopolymers (proteins and genetic sequences), but the exposition is not limited to them. A considerable effort has been made to render the volume comprehensible to researchers coming from either of the two hemispheres of bioinformatics: mathematics and computer science on one side, and biology, chemistry, and medicine on the other.Rather than an exhaustive coverage of the topic, which would be clearly impossible to do in just one book, the volume is intended as a snapshot of the latest research development and of the potentialities that operations research and machine learning techniques bring in this interdisciplinary field of research. Moreover, the volume aims at bridging the two mentioned halves of bioinformatics that are still quite disjoint, promoting a cross-fertilization hopefully fostering future research in the field.Primary selection criterion for the chapters has been scientific quality and importance. Additional selection criteria have been: (1) considering only approaches h...

Sequence distribution determination by SWAMP‐MS a systematic way of analyzing multiple fragmented polymers with mass spectrometry

“…MS is a powerful technique for the chemical characterization of polymers and excellent reviews have been written. [20][21][22][23][24] Matrix assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) are the most prominent ionization techniques used for MS for polymer research. 25 However, so far, all applied MS-MS methods to determine polymeric sequences are limited to the selection of a specific ion at rather low molecular weight values (5)(6)(7)(8)(9)(10).…”