The purpose of this program is aligning a query sequence against a sequence pattern. This method that is used is discussed above under Fastaswap and Fastapat. 150 Kb is not recommended. References Agarwal P, States DJ 1998 Comparative accuracy of methods for protein sequence similarity search. A protein alignment scoring system sensitive at all evolutionary distances.
Protein database searches for multiple alignments.
Basic local alignment search tool. Amino acid substitution matrices from an information theoretic perspective. A protein alignment scoring system sensitive at all evolutionary distances. Issues in searching molecular sequence databases. Information enhancement methods for large scale sequence analysis.