{"title":"Biological Sequence Analysis Using the SeqAn C++ Library","authors":"A. Gogol-Döring, K. Reinert","doi":"10.1201/9781420076240","DOIUrl":"https://doi.org/10.1201/9781420076240","url":null,"abstract":"An Easy-to-Use Research Tool for Algorithm Testing and Development Before the SeqAn project, there was clearly a lack of available implementations in sequence analysis, even for standard tasks. Implementations of needed algorithmic components were either unavailable or hard to access in third-party monolithic software products. Addressing these concerns, the developers of SeqAn created a comprehensive, easy-to-use, open source C++ library of efficient algorithms and data structures for the analysis of biological sequences. Written by the founders of this project, Biological Sequence Analysis Using the SeqAn C++ Library covers the SeqAn library, its documentation, and the supporting infrastructure. The first part of the book describes the general library design. It introduces biological sequence analysis problems, discusses the benefit of using software libraries, summarizes the design principles and goals of SeqAn, details the main programming techniques used in SeqAn, and demonstrates the application of these techniques in various examples. Focusing on the components provided by SeqAn, the second part explores basic functionality, sequence data structures, alignments, pattern and motif searching, string indices, and graphs. The last part illustrates applications of SeqAn to genome alignment, consensus sequence in assembly projects, suffix array construction, and more. This handy book describes a user-friendly library of efficient data types and algorithms for sequence analysis in computational biology. SeqAn enables not only the implementation of new algorithms, but also the sound analysis and comparison of existing algorithms. Visit SeqAn for more information.","PeriodicalId":282209,"journal":{"name":"Chapman and Hall / CRC mathematical and computational biology series","volume":"68 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128453091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Gene Expression Studies Using Affymetrix Microarrays","authors":"Hinrich W. H. Göhlmann, W. Talloen","doi":"10.1201/9781420065169","DOIUrl":"https://doi.org/10.1201/9781420065169","url":null,"abstract":"If you really want to be smarter, reading can be one of the lots ways to evoke and realize. Many people who like reading will have more knowledge and experiences. Reading can be a way to gain information from economics, politics, science, fiction, literature, religion, and many others. As one of the part of book categories, gene expression studies using affymetrix microarrays always becomes the most wanted book. Many people are absolutely searching for this book. It means that many love to read this kind of book.","PeriodicalId":282209,"journal":{"name":"Chapman and Hall / CRC mathematical and computational biology series","volume":"170 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124141634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R","authors":"G. Valiente","doi":"10.1201/9781420069747","DOIUrl":"https://doi.org/10.1201/9781420069747","url":null,"abstract":"Emphasizing the search for patterns within and between biological sequences, trees, and graphs, this book shows how combinatorial pattern matching algorithms can solve computational biology problems that arise in the analysis of genomic, transcriptomic, proteomic, metabolomic, and interactomic data. It provides an intuitive presentation of the algorithms, followed by a detailed exposition in pseudo-code. The author offers alternative implementations of the algorithms in Perl and R to enable the testing of algorithms and the building of projects based on the code. He also includes the Perl and R source code for all the algorithms on his website.","PeriodicalId":282209,"journal":{"name":"Chapman and Hall / CRC mathematical and computational biology series","volume":"59 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115944221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}