Every genome project generates thousands of ESTs or shotgun reads. Users have high interest in a first look at the DNA sequence content of the individual reads, before they are assembled (in case of shotgun reads) or clustered (in case of ESTs). Several steps are necessary to provide the researcher with high quality sequences, as well as an overview of their content. For all these purposes we have implemented some additional extensions to GenDB within the SAMS system.
SAMS is a simple, easy to install and maintain open source system that provides the mechanisms to run a variety of tools on each read/EST, presenting the results in a web form. The pipeline includes the processing of the raw sequence data (e.g. base calling, quality and vector clipping), the processing of ESTs using different tools (e.g. BLAST), and also the clustering and assembly of the sequences. Finally, the system provides a web based visualization of the results.
Further information about SAMS can be found on the SAMS homepage.
