Computer Analysis of Cloned Sequences

Analysis of the data generated from cDNA sequences, an important step in the final stages of any sequencing project, can provide insights into gene structure and function as well as help to direct the experimental approaches to obtaining the sequence of a full-length clone even when only preliminary data are available. The types of analyses that should be performed will depend on the immediate goal, and may evolve from trying to identify whether a clone is genuine or just an artifact to the stage where one would like to draw conclusions about function and domain structure of a previously unknown gene product encoded by the cDNA clone. This chapter provides an overview of the types of analyses that should be performed to extract the most information from a sequence. No attempt is made to review the current status of sequence analysis software, but particular programs are used to illustrate the general approaches that should be taken.