"Sequence Analysis and Management System" (SAMS)

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 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 EST pipeline is consisting of three parts. The preprocessing begins with importing the sequences, then running user-defined quality clipping, vector clipping against a standard database or custom sequences, and repeat masking. In the second part the pipeline continues with clustering the ESTs with user-specific parameters and afterwards the assembly is carried out, generating Tentative Consensus Sequences (TCs). Finally, the user can run the automatic annotation of the ESTs and TCs, which will launch BLAST searches against several database, such as KEGG and SwissProt, as well as InterPro and Pfam. Once the annotation is done, the user can manually go through it, checking for correctness.