A long standing problem in structural bioinformatics is to determine the three-dimensional (3-
D) structure of a protein when only a sequence of amino acid residues is given. Many …

With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the
computational challenge of efficiently and accurately constructing multiple genome …

AUGUSTUS is a software tool for gene prediction in eukaryotes based on a Generalized
Hidden Markov Model, a probabilistic model of a sequence and its gene structure. Like most …

Motivation: We introduce gmap, a standalone program for mapping and aligning cDNA
sequences to a genome. The program maps and aligns a single sequence with minimal …

Background In order to improve gene prediction, extrinsic evidence on the gene structure
can be collected from various sources of information such as genome-genome comparisons …

Although the R platform and the add-on packages of the Bioconductor project are widely
used in bioinformatics, the standard task of multiple sequence alignment has been …

Motivation Whole-genome alignment is an important problem in genomics for comparing
different species, mapping draft assemblies to reference genomes and identifying repeats …

Background A large number of gene prediction programs for the human genome exist.
These annotation tools use a variety of methods and data sources. In the recent ENCODE …

The responses of plants to abiotic stresses are accompanied by massive changes in
transcriptome composition. To provide a comprehensive view of stress‐induced changes in …

A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …