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