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Unique New Tool For Analyzing And Comparing Data - Created By Berkeley Scientists
Colleagues,
As reported in Medical News Today...Sung-Hou Kim, a chemist Berkeley Lab's Physical Biosciences Division and UC Berkeley's Chemistry Department, has led the development of a technique called "feature frequency profiles" (FFP), that makes it possible to compare, classify, index and catalog just about any type of linear information that can be electronically stored. The kinds of information that can be analyzed with the FFP technique include nucleotide base and amino acid sequences, books, documents and possibly images...
"I call our technique a tool for demographic phylogeny because it enables us to organize large sets of data into groups and find relationships among these groups," says Kim. "The idea is to organize data sets into groups based on the frequency at which key features occur and then look for relationships. This is the reverse of what is usually done, where you find relationships in the data set then organize the data set into groups based on those relationships."
Using the FFP technique, Kim and his colleagues can create "family trees" that put into easy-to-see perspective the relationships between groups within a data set, whether those groups are books or genomes. The key is to identify the "optimal features" for profiling. For books, the optimal feature consisted of sequences of text about eight letters in length. For mammalian genomes, the optical feature consisted of sequences of nucleotide bases of about 18 base pairs in length. However, to keep their genomic computations manageable, Kim and his colleagues reduced the four-letter DNA alphabet (adenine, guanine, thymine and cytosine) to a two-letter alphabet by using R for the purine nucleic acids and Y for the pyrimidine nucleic acids).
In a series of tests run on books and genomes, the FFP technique provided a more comprehensive and in some cases more accurate analysis over the standard analytical tools.
Kim is an internationally recognized authority on protein structures and a pioneer in the field of structural genomics. In 2003, he unveiled a 3-D demographic map of the protein structure universe that for the first time made it possible to organize the structures of this vast assemblage of biological molecules (more than 50 billion known species and growing) into meaningful groups.
"Scientists studying the genomes of different organisms are facing similar problems to those studying protein structures, perhaps even more difficult," Kim says. "Thousands of whole genomes have been or are in the process of being sequenced and we need to have an effective way of comparing and grouping them, and finding relationships among the groups. The FFP method can help us mine the function of gene-coding and non-coding nucleotide base sequences in the genome of a particular species, and can also give us a better understanding of how that species may have evolved, who its closest relatives are and other valuable information."
Read on at: http://www.medicalnewstoday.com/articles/138813.php
ENJOY!
CC
As reported in Medical News Today...Sung-Hou Kim, a chemist Berkeley Lab's Physical Biosciences Division and UC Berkeley's Chemistry Department, has led the development of a technique called "feature frequency profiles" (FFP), that makes it possible to compare, classify, index and catalog just about any type of linear information that can be electronically stored. The kinds of information that can be analyzed with the FFP technique include nucleotide base and amino acid sequences, books, documents and possibly images...
"I call our technique a tool for demographic phylogeny because it enables us to organize large sets of data into groups and find relationships among these groups," says Kim. "The idea is to organize data sets into groups based on the frequency at which key features occur and then look for relationships. This is the reverse of what is usually done, where you find relationships in the data set then organize the data set into groups based on those relationships."
Using the FFP technique, Kim and his colleagues can create "family trees" that put into easy-to-see perspective the relationships between groups within a data set, whether those groups are books or genomes. The key is to identify the "optimal features" for profiling. For books, the optimal feature consisted of sequences of text about eight letters in length. For mammalian genomes, the optical feature consisted of sequences of nucleotide bases of about 18 base pairs in length. However, to keep their genomic computations manageable, Kim and his colleagues reduced the four-letter DNA alphabet (adenine, guanine, thymine and cytosine) to a two-letter alphabet by using R for the purine nucleic acids and Y for the pyrimidine nucleic acids).
In a series of tests run on books and genomes, the FFP technique provided a more comprehensive and in some cases more accurate analysis over the standard analytical tools.
Kim is an internationally recognized authority on protein structures and a pioneer in the field of structural genomics. In 2003, he unveiled a 3-D demographic map of the protein structure universe that for the first time made it possible to organize the structures of this vast assemblage of biological molecules (more than 50 billion known species and growing) into meaningful groups.
"Scientists studying the genomes of different organisms are facing similar problems to those studying protein structures, perhaps even more difficult," Kim says. "Thousands of whole genomes have been or are in the process of being sequenced and we need to have an effective way of comparing and grouping them, and finding relationships among the groups. The FFP method can help us mine the function of gene-coding and non-coding nucleotide base sequences in the genome of a particular species, and can also give us a better understanding of how that species may have evolved, who its closest relatives are and other valuable information."
Read on at: http://www.medicalnewstoday.com/articles/138813.php
ENJOY!
CC
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