Gregory A Petsko
Gregory A Petsko
This unit offers an overview of issues that must be considered when analyzing molecular interactions. The importance of bound solvent, binding affinity, and electrostatic interactions is discussed.
DRAGON and DRAGON view: information annotation and visualization tools for large-scale expression data [0.03%]
DRAGON和DRAGON视图：大规模表达数据的信息注释与可视化工具
Christopher M L S Bouton,Jonathan Pevsner
Christopher M L S Bouton
The Database Referencing of Array Genes ONline (DRAGON) database system consists of information derived from publicly available databases including UniGene, SWISS-Prot, Pfam, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Through a...
Daniel H Huson
Daniel H Huson
A set of aligned character sequences or a matrix of evolutionary distances often contains a number of different and sometimes conflicting phylogenetic signals, and thus does not always support a unique tree. The method of split decompositio...
Using MODELTEST and PAUP* to select a model of nucleotide substitution [0.03%]
利用MODELTEST和PAUP＊选择核苷酸替代模型
David Posada
David Posada
Models of nucleotide substitution are commonly used in the analysis of DNA sequences. This unit describes the use of the program MODELTEST (coupled with PAUP*) to find the best-fit model of substitution for the sequence alignment at hand. A...
James C Wilgenbusch,David Swofford
James C Wilgenbusch
This unit provides a general description of reconstructing evolutionary trees using PAUP* 4.0. The protocol takes users through an example analysis of mitochondrial DNA sequence data using the parsimony and the likelihood criteria to infer ...
Roderic D M Page
Roderic D M Page
This unit provides a general introduction to phylogeny. It defines common terms and discusses the issue of rooting trees, in addition to comparing gene and species trees. Methods for inferring phylogenies, such as distance methods, parsimon...
Application of FirstEF to find promoters and first exons in the human genome [0.03%]
FirstEF在人类基因组中寻找启动子和第一个外显子的应用研究
Ramana V Davuluri
Ramana V Davuluri
Predicting first exons and promoters is an important part of gene finding in DNA sequence analysis. This unit presents FirstEF as a method for predicting the first exons and promoters. A combines FirstEF predictions with other information s...
Mark Borodovsky,Alex Lomsadze,Nikolai Ivanov et al.
Mark Borodovsky et al.
In this unit, eukaryotic GeneMark.hmm is presented as a method for detecting genes in eukaryotic DNA sequences. The eukaryotic GeneMark.hmm uses Markov models of protein coding and noncoding sequences, as well as positional nucleotide frequ...
Prokaryotic gene prediction using GeneMark and GeneMark.hmm [0.03%]
GeneMark和GeneMark.hmm软件包用于预测原核生物基因结构
Mark Borodovsky,Ryan Mills,John Besemer et al.
Mark Borodovsky et al.
In this unit, the GeneMark and GeneMark.hmm programs are presented as two different methods for the in silico prediction of genes in prokaryotes. GeneMark can be used for whole genome analysis as well as for the local analysis of a particul...
Victor Simossis,Jens Kleinjung,Jaap Heringa
Victor Simossis
Multiple sequence alignment is perhaps the most commonly applied bioinformatics technique. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families. In this u...