Showing papers by "Richard Durbin published in 2005"

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

Abstract: Probablistic models are becoming increasingly important in analyzing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analyzing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it is accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time presents the state of the art in this new and important field.

The DNA sequence of the human X chromosome

Abstract: The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.

The Sequence Ontology: a tool for the unification of genome annotations

Abstract: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a group of logical operations termed extensional mereology operators.

Acedb genome database

Abstract: Acedb is an integrative database system that has been widely used for management of genome oriented biological data. Since 1990, it has been used to manage and display the results of many of the large genome projects, starting with that for the nematode C. elegans from which it derives its name: A C Elegans DataBase. Acedb has many features to manipulate genomic sequence and other high genetic data, but also a flexible design that accommodates novel data types and attributes, and has been used for many other types of information, including those unrelated to biology. It provides an integrated research tool that requires no programming by the user to produce sophisticated representations and displays of genomic data. Keywords: genome database; C. elegans