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Parallel computation of genetic likelihoods using CRI-MAP, PVM, and a network of distributed workstations
T C Matise1, M D Schroeder, D M Chiarulli
1Department of Human Genetics, University of Pittsburgh, Pa 15261, USA.
Human Heredity
|March 1, 1995
Summary
We enhanced the CRI-MAP computer program for faster genetic linkage analysis. This parallel processing significantly speeds up the construction of genetic maps, keeping pace with new genotyping technologies.
Area of Science:
- Computational Biology
- Genetics
- Bioinformatics
Background:
- Genetic linkage analysis is crucial for mapping genes.
- Existing computational tools can be time-consuming for large datasets.
- Advances in genotyping necessitate faster analysis methods.
Purpose of the Study:
- To develop a parallelized version of the CRI-MAP program (CRI-MAP-PVM).
- To improve the efficiency of genetic likelihood computations.
- To accelerate the construction of genetic linkage maps.
Main Methods:
- Implemented parallel processing for CRI-MAP's FLIPS and ALL functions using PVM on a distributed network.
- Assessed performance using linkage analyses on human chromosome 1 with 85 microsatellite markers.
- Adapted the MultiMap program to utilize the parallelized CRI-MAP-PVM.
Main Results:
- CRI-MAP-PVM demonstrated excellent speedup and efficiency in linkage analyses.
- Low distribution overhead was observed.
- Significant reduction in the time required for comparing marker orders.
Conclusions:
- The parallelized CRI-MAP-PVM significantly accelerates genetic linkage map construction.
- This computational advancement supports rapid analysis in line with modern genotyping technologies.
- The improved efficiency aids researchers in timely gene mapping studies.