生物信息学技术

Abstract Table of Contents Figures Literature Cited Abstract MZEF (Michael Zhang's Exon Finder) was designed to help identify one of the most important classes of exons, i.e. the internal coding exons, in human genomic DNA sequences. It is

Abstract Table of Contents Materials Figures Literature Cited Abstract The Framesearch algorithm includes the possibility of a frameshift error in its alignment algorithm, and therefore can find alignment

Abstract Table of Contents Materials Figures Literature Cited Abstract The Clustal programs are widely used for carrying out automatic multiple alignment of nucleotide or amino acid sequences. The most fa

Abstract Table of Contents Materials Figures Literature Cited Abstract Blocks are ungapped multiple alignments of related protein sequence segments that correspond to the most conserved regions of the pro

Abstract Table of Contents Figures Literature Cited Abstract GlimmerM is a eukaryotic gene finder that has been used in the annotation of the genomes of Plasmodium falciparum (the malaria parasite), the model plant Arabidopsis thaliana, Or

Abstract Table of Contents Figures Literature Cited Abstract One of the major challenges in using bioinformatics software is that there are a wide variety of sequence formats, e.g., GenBank, EMBL, and FASTA. It is often the case that a seq

Abstract Table of Contents Materials Figures Literature Cited Abstract The MUMmer sequence alignment package is a suite of computer programs designed to detect regions of homology in long biological seque

Abstract Table of Contents Materials Figures Literature Cited Abstract PipMaker is a World?Wide Web site used to compare two long genomic sequences and identify conserved segments between them. This unit

Abstract Table of Contents Literature Cited Abstract Comparisons of whole genomes can yield important insights into the evolution of genome structure, such as the role of inversions in bacterial evolution and the identification of large?scale duplications in the human genom

Abstract Table of Contents Materials Figures Literature Cited Abstract There are several different methodologies that can be used for designing a database schema; no one is the best for all occasions. Thi

Abstract Table of Contents Materials Figures Literature Cited Supplementary Material Abstract Relational databases provide the most common platform for storing dat

Abstract Table of Contents Figures Literature Cited Abstract Models of nucleotide substitution are commonly used in the analysis of DNA sequences. This unit describes the use of the program MODELTEST (coupled with PAUundefined) to find the best?f

Abstract Table of Contents Figures Literature Cited Abstract This unit provides a general description of reconstructing evolutionary trees using PAUundefined 4.0. The protocol takes users through an example analysis of mitochondrial DNA sequence

Abstract Table of Contents Figures Literature Cited Abstract 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

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit discusses how the Accelrys GCG Wisconsin Package SeqLab graphical user interface can be used to align, annotate, analyze, a

Abstract Table of Contents Figures Literature Cited Abstract To understand how proteins work it is necessary to understand their physical state within the cell. This unit reviews the classification of proteins, how that is related to the h

Abstract Table of Contents Materials Figures Literature Cited Abstract A set of aligned character sequences or a matrix of evolutionary distances often contains a number of different and sometimes conflic

Abstract Table of Contents Figures Literature Cited Abstract 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 prom

Abstract Table of Contents Materials Figures Literature Cited Abstract Nuclease protection assays (S1 nuclease protection and RNase protection) are extremely sensitive procedures for detection and quantit

Abstract Table of Contents Figures Literature Cited Abstract As part of the Human Genome Variation Society (formerly known as the HUGO Mutation Database Initiative), a committee was formed to suggest standards for the description of sequen