SINGLE-BASE SEQUENCING AND SIMILARITY COMPARISONS

A ''single-base sequence'' is a DNA sequence in which the identities a nd locations of bases of only one type have been determined. We presen t experimental procedures for single-base sequencing and describe the effective use of existing software (FASTA) in similarity comparisons o f single-base sequences. We determined the theoretical and experimenta l minimum sequence lengths required for identification of a sequence w ithin a large dataset and optimized the FASTA parameters for use in si ngle-base similarity comparisons. Single-base sequences have been used to identify cDNAs occurring in a database. Single-base sequencing cou ld be used to reduce the redundancy of ''shotgun sequencing.'' (C) 199 5 Academic Press, Inc.