This technique was partially introduced to replace the use of PAM matrices and the FASTP program, and Progeniq has developed an FPGA version of this algorithm. The position-specific iterative version creates a list of strings closely related to the input, constructs a profile based on the list, searches the database, and repeats. The default value 
This technique was partially introduced to replace the use of PAM matrices and the FASTP program, and Progeniq has developed an FPGA version of this algorithm. The position-specific iterative version creates a list of strings closely related to the input, constructs a profile based on the list, searches the database, and repeats. The default value for the seed length in the first step of this algorithm is 11, and in the third stage uses the Smith-Waterman Algorithm to compute the MSP score. Inputs are commonly given in the FASTA format, and this algorithm is commonly used in evolutionary studies to construct phylogenetic trees. Also used to find relatives of genes and developed by Meyers and Altschul, for 10 points, name this bioinformatics algorithm used to compare protein or nucleotide sequences.
This technique was partially introduced to replace the use of PAM matrices and the FASTP program, and Progeniq has developed an FPGA version of this algorithm.
Basic Local Alignment Search Tool (BLAST)