Marco Pagni and Jörg Hau

Revision Date: 2008-01-18

Important Notice

This software and its documentation are copyrighted by the authors and are published under the terms and conditions of version 2 of the GNU Public License. The full text of this license is available on the 'About' page.

Please note that this license does not permit incorporating this program, or any part of it, into proprietary programs. If you do not understand any portion of this license, please seek appropriate professional legal advice. If you are not sure about these conditions, or if you do not or – for any reason – you can not accept all the conditions of this license, then do not use nor distribute this program. Or ... contact us, and we can work something out.

We would like to receive your comments about this software. If you have observed any errors or if you want to make constructive comments or contributions, please feel free to contact the authors via the official website of this project, http://hitkeeper.sourceforge.net.

Have fun!

Contents
1 Overview
 1.1 Introduction
 1.2 Some Definitions
 1.3 Commands, and the Seven Queries
 1.4 Codes, Identifers, and Synonyms
 1.5 Which database is searched?
2 Query Identifiers, and their Context
 2.1 Query Identifiers
 2.2 Context of Queries
3 Retrieval and Printing of Information
 3.1 fetch and dump
 3.2 Output Formats
4 Full-text Searches
 4.1 Purpose
 4.2 Syntax
5 Queries and full-text searches on sequences: seq_query
 5.1 Scope
 5.2 Out of Scope
 5.3 Options
6 Queries and full-text searches on motifs: mot_query
 6.1 Scope
 6.2 Out of Scope
 6.3 Options
7 Queries and full-text searches on classifications: cla_query
 7.1 Scope
 7.2 Out of Scope
 7.3 Options
8 Matching Sequences and Motifs: hit_query
 8.1 Scope
 8.2 How does it work?
 8.3 Options
9 Metamotifs, or “motifs of motifs”: mom_query
 9.1 Introduction
 9.2 Options
10 Metamotifs syntax
 10.1 About these examples
 10.2 The ’followed-by’ operator
 10.3 The ’report’ operator
 10.4 The ’curly bracket’ operator(s)
 10.5 The ’include’ operator
 10.6 Anchoring operators
 10.7 The ’motif-or’ operator
 10.8 The ’wildcard’ operator
 10.9 Length filter
 10.10 Signif filter
 10.11 Motif identifier
 10.12 Combining multiple filters
11 Sequences and Taxonomy: hat_query
 11.1 Scope
 11.2 Querying
 11.3 Options
12 Motifs and Taxonomy: It’s a hot_query
 12.1 Scope
 12.2 Querying
 12.3 Options
13 Limiting the number of results, setting a timeout
 13.1 Setting the Limits: Number of Results, Timeout
 13.2 Output Format
 13.3 Retrieving Query Results
Bibliography
Bibliography