Contents

• 1 Introduction
• 2 Installation and configuration
  • 2.1 Installation
  • 2.2 Description of files in the distribution
  • 2.3 Apache web server reconfiguration
  • 2.4 Database configuration
  • 2.5 Other configuration and log files
  
  
• 3 Structure and function of different web forms
  • 3.1 PSI/PHI Blast web form
  • 3.2 Client/server version for Entrez lookup and taxonomy reports
  • 3.3 XML output
  • 3.4 'Blast 2 sequences' page
  • 3.5 RPS BLAST
  • 3.6 Out of Frame BLASTX
  
  
• 4 Description of tags for the BLAST input web forms
  • 4.1 PROGRAM
  • 4.2 DATABASE
  • 4.3 QUERY
  • 4.4 SEQFILE
  • 4.5 INPUT_TYPE
  • 4.6 UNGAPPED_ALIGNMENT
  • 4.7 MAT_PARAM
  • 4.8 GAP_OPEN
  • 4.9 GAP_EXTEND
  • 4.10 X_DROPOFF
  • 4.11 GENETIC_CODE
  • 4.12 THRESHOLD_2
  • 4.13 MATRIX
  • 4.14 EXPECT
  • 4.15 NUM_OF_BITS
  • 4.16 NCBI_GI
  • 4.17 FILTER
  • 4.18 DESCRIPTIONS
  • 4.19 ALIGNMENTS
  • 4.20 COLOR_SCHEMA
  • 4.21 TAX_BLAST
  • 4.22 XML_OUTPUT
  • 4.23 ENTREZ_QUERY
  • 4.24 RPSBLAST
  • 4.25 OOF_ALIGN
  • 4.26 OTHER_ADVANCED
  • 4.27 ALIGNMENT_VIEW
  • 4.28 OVERVIEW
  • 4.29 BLAST_TYPE
  • 4.30 PHI_PATTERN
  • 4.31 TWEAK_PARAMETERS
  • 4.32 PHI_BLAST
  • 4.33 SMITH_WATERMAN
  • 4.34 E_THRESH
  • 4.35 MEGABLAST
  • 4.36 PERC_IDENT
  • 4.37 TEMPLATE_LENGTH
  • 4.38 TEMPLATE_TYPE
  • 4.39 TWO_HITS
  • 4.40 ENDPOINTS
  
  
• 5 Accessing wwwblast setup through URLAPI and scripting
• 6 Debug wwwblast programs
• 7 Technical support
• 8 Appendix
  • 8.1 Example httpd.conf for Apache
  • 8.2 Sample perl script
  
  
• Bibliography
• Index