Next:
1 Introduction
Up:
Program Parameters for blastall
Previous:
Program Parameters for blastall
Index
Contents
1 Introduction
1.1 What does blastall do?
1.2 How does blastall find the alignment?
1.3 Where can we find the blast program?
2 Installation and execution
2.1 For PC platform running Windows OS
2.2 For machines running Unix or Linux
2.3 For MacOSX
3 Program parameters for blastall
3.1 Presentation format
3.2 Individual command line options of blastall
4 General Usage
4.1 Nucleotide vs nucleotide search using blastn
4.2 Nucleotide vs protein search with blastx
4.3 4.3 Protein vs protein search with blastp
4.4 Protein vs nucleotide search with tblastn
4.5 Nucleotide vs nucleotide search with tblastx
4.6 Additional information and on searching with short queries
5 Scoring matrices, gap penalties, and others
5.1 Nucleotide scoring matrices and their -G/-E values
5.2 Protein scoring matrices and their -G/-E values
5.3 On -B option
6 Available BLAST alignment display formats
6.1 Header Section
6.2 Description section
6.3 Alignment section
6.4 Search Statistics Section
6.5 Other formats
7 Feedback
Bibliography
Index
Tao Tao 2006-12-29