Introduction

clasp is a fast and flexible fragment chainer that supports linear and sum-of-pair gap costs and uses highly time-efficient index structure, i.e., Johnson priority queues and range trees padded with Johnson priority queues. Chaining of short match fragments helps to quickly and accurately identify region of synteny that may not be found using common local alignment heuristics alone. Further details on the algorithm or the gap cost models are provided in Abouelhoda and Ohlebusch (2003).

It reads tab-separated fragment files providing information on fragment start and end position on query and database sequence as well as a score measure. It executes a local chaining algorithm using either the linear (parameter -L, --lin) or the sum-of-pair gap cost model (default). It produces a tab-separated output of chain data, optionally including fragments. Note that the algorithm is optimized for short queries and large database sequences using a novel clustering approach.

Download

• clasp_v1_1.tar.gz (bugfix of parameter option --orig)
• clasp_v1_0.tar.gz (initial release)

Installation

Example (with BLAST)

Run BLAST

Chain blast output

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