1 Introduction

This document contains tutorial material for HitKeeper. It is part of a workshop that was (is) held by the authors of HitKeeper .

HitKeeper ( http://hitkeeper.sourceforge.net/) is a collection of software tools, originally designed for the investigation of the relationships between protein sequences and motifs on them. It is designed to help researchers in the laboratory with “friendly” bioinformatics tools, automating parts of a repetitive workflow.

HitKeeper implements an elaborate query syntax to retrieve information. These queries enable the user to express any constraints for searching proteins, such as retrieving sequences that contain specific motifs, or a defined arrangement of motifs (“metamotifs”), or queries based on the classification of sequences (to focus e.g. on taxonomy or an alternative classification). This tutorial is meant to progressively introduce the syntax and the associated concepts, featuring a not-too-steep learning curve.