Algorithms in Bioinformatics

Algorithms in Bioinformatics

An improved model for statistical alignment (I. Mikls, Z. Toroczkai). Improving profile-profile alignments via log average scoring (N. von ohsen, R. Zimmer). False positive s in genomic map assembly and sequence validation (T. Anantharaman, B. Mishra). Boosting EM for radiation hybrid and genetic mapping (T. Schiex, P. Chabrier, M. Bouchez, D. Milan). Placing probes along the genome using pairwise distance data (W. Casey, B. Mishra, M. Wigler). Comparing a Hidden Markov model and a stochastic context-free grammar (A. Jagota, R. B. Lyngso, C. N. S. Pedersen). Assessing the statistical significance of overrepresented oligonucleotides (A. Denise, M. Rgnier, M. vandenbogaert). Pattern matching and pattern discovery algorithms for protein topologies (J. Viksna, D. Gilbert). Computing linking numbers of a filtration (H. Edelsbrusnner, A. Zomorodian). Side chain-positioning as an integer programming problem (O. Eriksson, Y. Zhou, A. Elofsson). A chemical-distance-based test for positive darwinian selection (T. Pupko, R. Sharan, M. Hasegawa, R. Shamir, D. Graur). Finding a maximum compatible tree for a bounded number of trees with bounded degree is solvable in polynominal time (G. Ganapathysaravanabavan, T. Warnow). Experiments in computing sequences of reversals (A. Bergeron, Franois Strasbourg). Exact-IEBP: a new technique for estimating evolutionary distances between whole genomes (Li-San Wang). Finding an optimal inversion median: experimental results (A. C. Siepel, B. M. E. Moret). Analytic solutions for three-taxon MLMC trees with variable rates across sites (B. Chor, M. Hendy, D. Penny). The performance of phylogenetic methods on trees of bounded diameter (L. nakhleh, U. Roshan, K. St. John, J. Sun, T. Warnow). (1+E)- approximation of sorting by reversals and transpositions (N. Eriksen). On the practical solution of the reversal median problem (A. Caprara). Algorithms for finding gene clusters (S. Heber, J. Stoye). Determination of binding amino acids based on random peptide array screening data (P. J. van der Veen, L. F. A. Wessels, J. W. Sloostra, R. H. Meloen, M. J. T. Reinders, J. Hellendoorn). A simple hyper-geometric approach for discovering putative transcription factor binding sites (Y. Barash, G. Bejerano, N. Friedman). Comparing assemblies using fragments and mate-pairs (D. H. Huson, A. L. Halpern, Z. Lai, E. W. myers, K. Reinert, G. G. Sutton). Author index.

Algorithms in Bioinformatics

Advanced Oil Crop Biorefineries

Advanced Oil Crop Biorefineries

In Europe, the main oil-rich crops are sunflower, rapeseed and olive which are grown primarily for food. This book discusses how to convert this whole crop into energy (fuels, power and heat), food and bioproducts (chemicals and/or materials), whilst making optimal use of the by-products generated during farming/harvesting, primary processing (oil extraction and refining) and secondary processing (transesterification). The resulting processes are more economically competitive and the business margin for oil and biodiesel manufacturers is improved. Previously, oil crops have been the main point of focus but many of the technologies used are applicable to a wide variety of raw materials. For example, cellulose from rapeseed straw can be converted to levulinic acid but the same technology could be applied to cellulose from wheat straw or wood. Significant effort is now being devoted to ‘2nd generation’ raw materials such as ligno-cellulose which avoid direct competition with food sources. This volume integrates these developments with existing plant oil supply chains and combines biochemical and thermochemical processes to form integrated biorefinery schemes. Two unique features of the book are the information on LCA of biorefinery schemes and the surveys showing where traditional industries could be affected by new biorefinery developments. Energy and cost calculations for the key biorefinery processes and are also included revealing that some are surprisingly profitable and could offer significant global benefits. Other topics covered include: novel farming and harvesting methods, efficient extraction of plant oils, producing biodiesel without glycerol, extraction of high value chemicals from agricultural by-products, anaerobic digestion potential of agricultural by-products, use of proteins to yield amino acids, economics and life cycle analysis, stakeholder surveys, and policy scenarios. The book is of interest to academics working in relevant areas of chemistry, biology, materials, engineering, economics and policy studies. Those working in the EU farming industry will also find it relevant to their business.

Advanced Oil Crop Biorefineries