D E Foulser | PubMed Health

PubMed1990

Parallel computation of multiple biological sequence comparisons.

A parallel implementation of an efficient method for comparison of multiple DNA sequences is presented. The method is described in terms of a conceptual tree data structure for the sequences to be compared. The parallel algorithm shows efficient utilization of processors on an Encore Multimax computer in a sample comparison of 11 sequences totaling over 4000 bases. Timing data show the strong influence of computer system details on this parallel program. Also presented is a graphics program for displaying multiple sequence comparison output data. The display is capable of representing large volumes of multiple sequence comparison data in a single plot. The program has several additional features that allow closer examination of subsets of sequences. A display of matches from the sample comparison reflects the known structure of these sequences.

Algorithms↗

PubMed1985

DNA sequence comparisons of the human, mouse, and rabbit immunoglobulin kappa gene.

A comparative analysis between human, mouse, and rabbit immunoglobulin (Ig) kappa-gene DNA sequences is presented. New formulas for determining the expected length and variance of the longest block identity (a succession of matching nucleotides) between multiple random sequences are given and are used to establish statistical criteria for ascertaining the significance of block identities shared in r out of s sequences. The statistically significant block identities within and between the Ig-kappa-gene sequences are ascertained, and alignment maps based on these similarities are constructed. The human and rabbit sequences (especially in the noncoding regions) and the human and mouse sequences (on the coding regions) show a similarity much stronger than that between the mouse and rabbit sequences. The existence of several highly significant shared oligonucleotides occurring in alignment with each other or with respect to the J- and C-gene segments suggests a configuration of multiple control sites. Discussion and interpretations of the form and distribution of the block identities are given.

Animals↗