ABSTRACT
BLASTN, BLASTP, BLASTX, and TBLASTN have been introduced in the last three chapters and you now have experience to address a variety of sequence analysis tasks and problems. This chapter will extend this experience by addressing additional problems of gene identity and structure. Importantly, BLAST parameters will be varied to help identify sequences missed by the default settings. As they are frequently encountered during sequence analysis, several families of repetitive DNA will be described to better prepare you for the unexpected. Finally, a summary of guidelines is presented to assist when making decisions about distant relationships based on sequence similarity.
