Sequence Similarity Searching Using the BLAST Family of Programs
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
Database sequence similarity searching is carried out thousands of times each day by researchers worldwide and has become a very valuable tool. Over the years, a number of algorithms have been implemented to facilitate database searching. The BLAST (Basic Local Alignment Research Tool) family of sequence similarity search programs allows searches to be done quickly and easily, but with sensitive, yet rigorous statistical expectations. In this unit, which is a completely new version of its predecessor of the same title, the user learns how to access the databases, determine the correct searching strategies, and apply examples of BLAST searches to his or her own data.
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PDF or HTML at Wiley Online LibraryTable of Contents
- Accessing BLAST Programs and Documentation
- Introduction to BLAST
- Examples of BLAST Searches
- Searching Strategies
- Sequence Alignment Algorithms
- Appendix A: BLAST Parameters
- Appendix B: Sequence Identifier Syntax
- Literature Cited
- Figures
- Tables
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Figure 19.3.1 Submitting a BLASTP search using the NCBI's World Wide Web interface. View Image -
Figure 19.3.2 Example of the top portion of a BLASTP report. View Image -
Figure 19.3.3 Example of the graphical view of a BLASTP report. The bars are color coded by the strength of the database match. The strongest matches (those with a bit score >200) are red, followed by pink (bit score 80 to 200), green (50 to 80), blue (40 to 50), and black (<40). View Image -
Figure 19.3.4 Example of the hit list from a BLASTP report. View Image -
Figure 19.3.5 Example of a BLASTP alignment. View Image -
Figure 19.3.6 Example of the graphical view of a BLASTX report. View Image -
Figure 19.3.7 Example of the hit list from a BLASTX report. View Image -
Figure 19.3.8 Example of selected BLASTX alignments. View Image -
Figure 19.3.9 Example of the graphical view of a TBLASTN report. View Image -
Figure 19.3.10 Example of the hit list from a TBLASTN report. View Image -
Figure 19.3.11 Example of a TBLASTN alignment. View Image -
Figure 19.3.12 Example of the graphical view of a BLASTN report. View Image -
Figure 19.3.13 Example of the hit list from a BLASTN report. View Image -
Figure 19.3.14 Example of a BLASTN alignment. View Image -
Figure 19.3.15 Example of the hit list from a PSI‐BLAST report. View Image -
Figure 19.3.16 Example of a hit list from a BLASTP report in which the query sequence was not filtered. Black squares, added manually by the authors, indicate hits that would not appear if the query had been filtered. View Image
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Literature Cited
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