ABSTRACT

An Easy-to-Use Research Tool for Algorithm Testing and DevelopmentBefore the SeqAn project, there was clearly a lack of available implementations in sequence analysis, even for standard tasks. Implementations of needed algorithmic components were either unavailable or hard to access in third-party monolithic software products. Addressing these conc

part |2 pages

I The SeqAn Project

chapter 1|12 pages

Background

chapter 2|8 pages

SeqAn

chapter 3|6 pages

Library Design

chapter 4|18 pages

Programming Techniques

chapter 5|16 pages

The Design in Examples

part |2 pages

II Library Contents

chapter 6|14 pages

Basics

chapter 7|26 pages

Sequences

chapter 8|30 pages

Alignments

chapter 9|28 pages

Pattern Matching

chapter 10|20 pages

Motif Finding

chapter 11|28 pages

Indices

chapter 12|18 pages

Graphs

part |2 pages

III Applications

chapter 13|10 pages

Aligning Sequences with LAGAN

chapter 14|8 pages

Multiple Alignment with Segments

chapter 15|12 pages

Basic Statistical Indices for SeqAn

chapter 16|22 pages

A BWT-Based Suffix Array Construction