Accessing Files of Sequences from Databases
in Perl for Exploring DNA
August 2007; published online April 2010.
Chapter. Subjects: biomathematics. 4312 words.
This chapter gives instructions for getting to the vast databases of NCBI and coming away with the files of sequence wanted. Sequence databases are the new museums of the genomic age. The grandest of...
Advanced Topics in Systems Biology and Network Evolution
in Statistical Theory and Methods for Evolutionary Genomics
November 2010; published online January 2011.
Chapter. Subjects: biomathematics. 15404 words.
As evolutionary biologists have always been concerned with the genetic basis for the emergence of complex phenotypes, advances in genomics and systems biology are facilitating a paradigm shift of...
Arrays
in Perl for Exploring DNA
August 2007; published online April 2010.
Chapter. Subjects: biomathematics. 6088 words.
This chapter is about scaling up. It introduces a list-like data structure used to collect and manage large numbers of DNA files and sequences for analysis. Any analysis that can be done on a single...
Basics in Bioinformatics and Statistics
in Statistical Theory and Methods for Evolutionary Genomics
November 2010; published online January 2011.
Chapter. Subjects: biomathematics. 6137 words.
The available web-based genome resources provide great opportunities for biomedical scientists to identify functional elements in a particular genome region or explore the evolutionary pattern of...
Basics in Molecular Evolution
in Statistical Theory and Methods for Evolutionary Genomics
November 2010; published online January 2011.
Chapter. Subjects: biomathematics. 14664 words.
Molecular evolution is the study of the process of evolution at the level of DNA, RNA, and proteins, in which the neutral or nearly neutral evolution model has provided the theoretical basis. Yet,...
Conclusions
in Perl for Exploring DNA
August 2007; published online April 2010.
Chapter. Subjects: biomathematics. 893 words.
Anton van Leeuwenhoek, the microscopist, was in great demand as a party guest in fashionable Delft homes in the 17th century. He could be counted upon to bring along several hand-held microscopes...
Essential First Steps: Installing Perl Plus a Programming Environment
in Perl for Exploring DNA
August 2007; published online April 2010.
Chapter. Subjects: biomathematics. 1054 words.
Clear directions for Mac OS X and Windows users alike are provided to get these respective hardware systems set up for programming in Perl. This chapter provides as much encouragement and support as...
Expression between Duplicate Genes: Genome‐Wide Analysis
in Statistical Theory and Methods for Evolutionary Genomics
November 2010; published online January 2011.
Chapter. Subjects: biomathematics. 4938 words.
Expression divergence between duplicate genes has long been a subject of great interest to geneticists and evolutionists. Ohno proposed that expression divergence is the first step in the functional...
Functional Divergence after Gene Duplication: Applications and Others
in Statistical Theory and Methods for Evolutionary Genomics
November 2010; published online January 2011.
Chapter. Subjects: biomathematics. 6985 words.
As most amino acid substitutions are not related to the functional divergence but only represent the neutral evolution, it becomes crucial how to distinguish statistically between these two...
Functional Divergence after Gene Duplication: Statistical Modeling
in Statistical Theory and Methods for Evolutionary Genomics
November 2010; published online January 2011.
Chapter. Subjects: biomathematics. 10787 words.
Many organisms have undergone genome-wide or local chromosome duplication events during their evolution. As a result, many genes are represented as several paralogs in the genome with related but...