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On-Demand Indexing for Referential Compression of DNA Sequences.

Alves F, Cogo V, Wandelt S, Leser U, Bessani A - PLoS ONE (2015)

Bottom Line: Referential compression is one of these techniques, in which the similarity between the DNA of organisms of the same or an evolutionary close species is exploited to reduce the storage demands of genome sequences up to 700 times.The general idea is to store in the compressed file only the differences between the to-be-compressed and a well-known reference sequence.Our approach, called On-Demand Indexing (ODI) compresses human chromosomes five to ten times faster than other state-of-the-art tools (on average), while achieving similar compression ratios.

View Article: PubMed Central - PubMed

Affiliation: LaSIGE, University of Lisbon, Lisbon, Portugal.

ABSTRACT
The decreasing costs of genome sequencing is creating a demand for scalable storage and processing tools and techniques to deal with the large amounts of generated data. Referential compression is one of these techniques, in which the similarity between the DNA of organisms of the same or an evolutionary close species is exploited to reduce the storage demands of genome sequences up to 700 times. The general idea is to store in the compressed file only the differences between the to-be-compressed and a well-known reference sequence. In this paper, we propose a method for improving the performance of referential compression by removing the most costly phase of the process, the complete reference indexing. Our approach, called On-Demand Indexing (ODI) compresses human chromosomes five to ten times faster than other state-of-the-art tools (on average), while achieving similar compression ratios.

No MeSH data available.


Percentage of the reference indexed by each tool.FRESCO always indexes the full reference (100% for all chromosomes). The percentage of the reference indexed by JDNA varies per chromosome, but is always less than 10%.
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pone.0132460.g006: Percentage of the reference indexed by each tool.FRESCO always indexes the full reference (100% for all chromosomes). The percentage of the reference indexed by JDNA varies per chromosome, but is always less than 10%.

Mentions: Fig 6 presents the percentage of each reference chromosome sequence indexed by each tool. JDNA is able to compress individual genomes indexing less than 10% of each chromosome, where the average percentage is only 2.5%. It reinforces the idea that more than 90% of each chromosome is indexed without a significant contribution to the overall compression process.


On-Demand Indexing for Referential Compression of DNA Sequences.

Alves F, Cogo V, Wandelt S, Leser U, Bessani A - PLoS ONE (2015)

Percentage of the reference indexed by each tool.FRESCO always indexes the full reference (100% for all chromosomes). The percentage of the reference indexed by JDNA varies per chromosome, but is always less than 10%.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493149&req=5

pone.0132460.g006: Percentage of the reference indexed by each tool.FRESCO always indexes the full reference (100% for all chromosomes). The percentage of the reference indexed by JDNA varies per chromosome, but is always less than 10%.
Mentions: Fig 6 presents the percentage of each reference chromosome sequence indexed by each tool. JDNA is able to compress individual genomes indexing less than 10% of each chromosome, where the average percentage is only 2.5%. It reinforces the idea that more than 90% of each chromosome is indexed without a significant contribution to the overall compression process.

Bottom Line: Referential compression is one of these techniques, in which the similarity between the DNA of organisms of the same or an evolutionary close species is exploited to reduce the storage demands of genome sequences up to 700 times.The general idea is to store in the compressed file only the differences between the to-be-compressed and a well-known reference sequence.Our approach, called On-Demand Indexing (ODI) compresses human chromosomes five to ten times faster than other state-of-the-art tools (on average), while achieving similar compression ratios.

View Article: PubMed Central - PubMed

Affiliation: LaSIGE, University of Lisbon, Lisbon, Portugal.

ABSTRACT
The decreasing costs of genome sequencing is creating a demand for scalable storage and processing tools and techniques to deal with the large amounts of generated data. Referential compression is one of these techniques, in which the similarity between the DNA of organisms of the same or an evolutionary close species is exploited to reduce the storage demands of genome sequences up to 700 times. The general idea is to store in the compressed file only the differences between the to-be-compressed and a well-known reference sequence. In this paper, we propose a method for improving the performance of referential compression by removing the most costly phase of the process, the complete reference indexing. Our approach, called On-Demand Indexing (ODI) compresses human chromosomes five to ten times faster than other state-of-the-art tools (on average), while achieving similar compression ratios.

No MeSH data available.