High performance distributed computing: an introduction.
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Computer Communication Networks↗
Biomedical subjects
R M Abarbanel
Publications and source records attributed to R M Abarbanel.
Biomedical database inter-connectivity: an experiment linking MIM, GENBANK, and META-1 via MEDLINE.
The linkage of disparate biomedical databases is an important goal of the Unified Medical Language (UMLS) Project. We conducted an experiment to investigate the feasibility of using UMLS resources to link databases in clinical genetics and molecular biology. References from MIM ("Mendelian Inheritance in Man") were lexically mapped to the equivalent citations in MEDLINE. The MeSH major subject headings by which the citations in a particular MIM entry had been indexed were used to develop a "genetic-disorder-centered view of the world" in Meta-1 (the first official version of the UMLS Metathesaurus). Our hypothesis was that these MeSH subject headings could provide access to a "semantic neighborhood" in Meta-1 that would be relevant to a particular genetic disorder. By browsing in this "semantic neighborhood," a user could select various combinations of terms with which to search MEDLINE through an interface between Meta-1 and Grateful Med. Such searches might retrieve citations that were more recent than those in MIM or that provided useful supplementary information. Since some MEDLINE records contain pointers to entries in GENBANK, information about genetic sequences related to a particular clinical genetic disorder could also be retrieved. This scenario was implemented for a small number of MIM entries, providing a concrete demonstration that linking disparate electronic databases in an important subdomain of biomedicine is relatively straightforward.
Databases, Factual↗
Turn prediction in proteins using a pattern-matching approach.
We extend the use of amino acid sequence patterns [Cohen, F.E., Abarbanel, R. M., Kuntz, I. D., & Fletterick, R. J. (1983) Biochemistry 22, 4894-4904] to the identification of turns in globular proteins. The approach uses a conservative strategy, combined with a hierarchical search (strongest patterns first) and length-dependent masking, to achieve high accuracy (95%) on a test set of proteins of known structure. Applying the same procedure to homologous families gives a 90% success rate. Straightforward changes are suggested to improve the predictive power. The computer program, written in Lisp, provides a general pattern-recognition language well suited for a number of investigations of protein and nucleic acid sequences.
Amino Acid Sequence↗
Rapid searches for complex patterns in biological molecules.
The intrinsic redundancy of genetic information makes searching for patterns in biological sequences a difficult task. We have designed an interactive self-documenting computer program called QUEST that allows rapid searching of large DNA and protein data banks for highly redundant consensus sequences or character patterns. QUEST uses a concise language for specifying character patterns containing several levels of ambiguity and pattern arrangement. Examples of the use of this program for sequence data are given. Details of the algorithm and pattern optimization are explained.
Amino Acid Sequence↗
Secondary structure assignment for alpha/beta proteins by a combinatorial approach.
We describe an algorithm for assigning the secondary structure of alpha/beta proteins. Turns are identified very accurately (98%) by simultaneously considering hydrophilicity and the ideal spacing of turns throughout the sequence. The segments bounded by these turns are labeled by a pattern-recognition scheme based on the physical properties of alpha-helices and beta-strands, in this class of proteins. Long-range, as well as local, information is incorporated to enhance the quality of the assignments. Although the assignment for any one sequence is not unique, at least one of the assignments bears a close resemblance to the native structure. The algorithm successfully divides protein sequences into two classes: alpha/beta and non-alpha/beta. The accuracy of the secondary-structure assignments in the alpha/beta class is sufficient to provide useful input for tertiary-structure assignments.
Isomerism↗
Malignant melanoma of the skin. I. The association of tumor depth and type, and patient sex, age, and site with survival.
The occurrence and behavior of cutaneous melanomas in a group of 1123 patients studied prospectively, is described in terms of histologic type, tumor thickness and levels of invasion, the patients' sex and age, and the anatomic location of the primary tumors. Associations amongst these attributes, and with survival, are also examined. The characteristics of the patients in this study (who on average are somewhat younger, and have better prognoses and survivals than those reported by most other groups) are compared with data obtained (primarily over the past decade) in other geographical areas, and with different patient populations. Evidence is presented that sex, tumor location, and age (in the case of males) are also predictive of survival.
Adolescent↗