Improved processors and processing methods are disclosed for high-speed computerized comparison analysis of multiple linear symbol or character sequences, such as biological nucleic acid sequences, protein sequences, or other long linear arrays of characters. These improved processors and processing methods, which are suitable for use with recursive analytical techniques such as the Smith-Waterman algorithm, and the like, are optimized for minimum gate count and maximum clock cycle computing efficiency. This is done by interleaving multiple linear sequence comparison operations per processor, which optimizes use of the processor's resources. In use, a plurality of such processors are embedded in high-density integrated circuit chips, and run synchronously to efficiently analyze long sequences. Such processor designs and methods exceed the performance of currently available designs, and facilitate lossless higher dimensional sequence comparison analysis between three or more linear sequences.