Databank Search and Multiple Sequence Alignment

1997/8/19


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目錄

Databank Search and Multiple Sequence Alignment

Why do you want to do a databank search?

Criteria to Evaluate A Database Searching Program

Popular Programs

A typical FastA Output Has Three Components

How to interprete the FastA Histogram

The FastA Histogram

Signal vs Noise

Review of Simple Statistics

Rules of Thumb (I)

When do you care about the statistical significance?

List of Related Sequences

FastA Alignments

Rules of Thumb (II)

Pearson’s Suggestion

What is k-tuple?

Large k-tuple Will Lose Sensitivity

Effect of k-tuple on Matching

Effect of k-tuple on Inital Scores

Major Steps in FastA

Summary: FastA Algorithm

Effect of ktup to FastA Output

Summary: FastA Statistics

Limitation of FastA

BLAST

A Typical Blast Output Does Not Include A Histogram

The Statistical Significance Can Be Directly Calculated from? the Score of HSP

HSP & MSP

List of Related Sequences of A Typical Blast Output

When you get more than 1000 significant sequences, ?you may need filters.

Assumption of Program Blast

Two Ways to Eliminate the Violations of Assumption

Effect of Filters

Blast Alignments

FastA Alignments

The Advantage of Searching a Protein Databank or Translated Nucleic Acid Databank

The End

Databank Searching

Mutation Matrix

Concepts

作者: 楊永正

電子郵件: yang@ym.edu.tw

首頁: http://140.110.34.65/binfo-i/slides.htm

其他資訊:
If you have any question or comments, please connect with us.

Tel: (03)577-6085 ext 328 劉玉凡

Tel: (02) 826-7128 楊永正教授

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