Document Detail


ParaSAM: a parallelized version of the significance analysis of microarrays algorithm.
MedLine Citation:
PMID:  20400455     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MOTIVATION: Significance analysis of microarrays (SAM) is a widely used permutation-based approach to identifying differentially expressed genes in microarray datasets. While SAM is freely available as an Excel plug-in and as an R-package, analyses are often limited for large datasets due to very high memory requirements. SUMMARY: We have developed a parallelized version of the SAM algorithm called ParaSAM to overcome the memory limitations. This high performance multithreaded application provides the scientific community with an easy and manageable client-server Windows application with graphical user interface and does not require programming experience to run. The parallel nature of the application comes from the use of web services to perform the permutations. Our results indicate that ParaSAM is not only faster than the serial version, but also can analyze extremely large datasets that cannot be performed using existing implementations. AVAILABILITY: A web version open to the public is available at http://bioanalysis.genomics.mcg.edu/parasam. For local installations, both the windows and web implementations of ParaSAM are available for free at http://www.amdcc.org/bioinformatics/software/parasam.aspx.
Authors:
Ashok Sharma; Jieping Zhao; Robert Podolsky; Richard A McIndoe
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2010-04-15
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  26     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2010 Jun 
Date Detail:
Created Date:  2010-05-20     Completed Date:  2010-09-02     Revised Date:  2010-09-28    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  1465-7     Citation Subset:  IM    
Affiliation:
Center for Biotechnology and Genomic Medicine, School of Medicine, Medical College of Georgia, Augusta, GA 30912, USA.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Databases, Factual
Oligonucleotide Array Sequence Analysis / methods*
Software*
Grant Support
ID/Acronym/Agency:
U24DK076169/DK/NIDDK NIH HHS
Comments/Corrections

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