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Bioinformatics
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Страница 1
Table of Contents
List of Tables
List of Illustrations
Guide
Pages
Bioinformatics
Страница 8
Foreword
Preface
Contributors
About the Companion Website
1 Biological Sequence Databases
Introduction
Nucleotide Sequence Databases
Nucleotide Sequence Flatfiles: A Dissection
The Header
Box 1.1
Functional Divisions in Nucleotide Databases
The Feature Table
Graphical Interfaces
RefSeq
Box 1.2
RefSeq
Protein Sequence Databases
The NCBI Protein Database
UniProt
Summary
Box 1.3
Ensuring the Continued Quality of Data in Public Sequence Databases
Acknowledgments
Internet Resources
Further Reading
References
2 Information Retrieval from Biological Databases
Introduction
Integrated Information Retrieval: The Entrez System
Relationships Between Database Entries: Neighboring
Hard Links
The Entrez Discovery Pathway
Medical Databases
Organismal Sequence Databases Beyond NCBI
Summary
Internet Resources
Further Reading
References
3 Assessing Pairwise Sequence Similarity: BLAST and FASTA
Introduction
Global Versus Local Sequence Alignments
Scoring Matrices
Box 3.1
Scoring Matrices and the Log Odds Ratio
PAM Matrices
BLOSUM Matrices
Which Matrices Should be Used When?
Nucleotide Scoring Matrices
Gaps and Gap Penalties
BLAST
The Algorithm
Box 3.2
The Karlin–Altschul Equation
Performing a BLAST Search
Understanding the BLAST Output
Suggested BLAST Cut-Offs
BLAST 2 Sequences
MegaBLAST
PSI-BLAST
The Method
Performing a PSI-BLAST Search
BLAT
FASTA
The Method
Running a FASTA Search
Statistical Significance of Results
Comparing FASTA and BLAST
Summary
Internet Resources
Further Reading
References
4 Genome Browsers
Introduction
The UCSC Genome Browser
Box 4.1
Common File Types for Genomic Data
Box 4.2
GENCODE
Box 4.3
Histone Marks
UCSC Table Browser
ENSEMBL Genome Browser
Box 4.4
Ensembl Stable IDs
Ensembl Biomart
JBrowse
Summary
Internet Resources
Further Reading
References
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