Fast analysis of DNA and protein sequence on Apple IIe: restriction sites search, alignment of short sequence and dot matrix analysis.
A fast restriction sites search algorithm using a quadruplet look-ahead feature has been written in 6502 assembly language code. The search time, tested on the sequence of pBR322, is 4.1 s/kilobase using a restriction site library including 112 specificities corresponding to a total site length of over 700 bases. The search for a short sequence (less than 36 bases) within a longer one (up to 9999 bases) with a given number of mismatches or gaps allowed has also been written in assembly language. Typical run time for the search of a 12 base sequence with 1, 2 or 3 gaps allowed are 6.2, 9.4 or 13.6 s/kilobase, respectively. The dot matrix analysis needs 7.5 minutes per square kilobase when using a stringency of 15 matched bases out of 25. A 7/21 matrix of two 500 amino acid proteins is obtained in 3 minutes. These three routines are included in DPSA, a general package of programs allowing manipulation and analysis of DNA and protein sequences.
D000595:Amino Acid Sequence; D001483:Base Sequence; D003201:Computers; D004247:DNA / Q000032:analysis*; D004262:DNA Restriction Enzymes / Q000378:metabolism; D008838:Microcomputers; D011506:Proteins / Q000032:analysis*; D012984:Software
D011506:Proteins; D004247:DNA; D004262:DNA Restriction Enzymes