Contents

• 1 User Requirements
• 2 Introduction
• 3 Quick Start
  • 3.1 Put: Pushes A Search Request With Custom Settings Into splitd
  • 3.2 Get: Retrieves Results Using the Assigned RID
  
  
• 4 Commands
  • 4.1 Put
  • 4.2 Get
  • 4.3 Info
  
  
• 5 Parameters
  • 5.1 Information on Individual URLAPI Parameters
  
  
• 6 Combinations of Parameters and Their Effects
  • 6.1 Number of Alignments Returned
  • 6.2 RID for Simultaneous CDD Search
  • 6.3 Entrez Query Terms
  • 6.4 Filter Strings: Functions and Alignment Display
  • 6.5 MEGABLAST Features
  • 6.6 Converting PSSMS
  • 6.7 Options and Values for 'OTHER_ADVANCED'
  • 6.8 Show Overview
  • 6.9 Display of Description Section
  • 6.10 HSP Sorting in the Alignment Section
  • 6.11 Display of CDS and Linkout Icons
  • 6.12 Template Length and Type
  • 6.13 On Matrices and Gapcosts
  • 6.14 Pattern Syntax for PHI-BLAST
  • 6.15 Searching with Short Queries
  
  
• 7 Compatibility
• 8 Additional Information
  • 8.1 User Requirements
  • 8.2 Error Checking
  • 8.3 Escape of Unsafe Characters
  • 8.4 Example Search (Put) URLs
  • 8.5 Example Retrieval (Get) URLs
  • 8.6 Sample Script in Perl
  
  
• 9 Summary
• Bibliography
• Index