↓ Skip to main content

Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays

Overview of attention for article published in Algorithms for Molecular Biology, April 2016
Altmetric Badge

About this Attention Score

  • Average Attention Score compared to outputs of the same age

Mentioned by

twitter
3 X users

Citations

dimensions_citation
2 Dimensions

Readers on

mendeley
13 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
Bitpacking techniques for indexing genomes: II. Enhanced suffix arrays
Published in
Algorithms for Molecular Biology, April 2016
DOI 10.1186/s13015-016-0068-6
Pubmed ID
Authors

Thomas D. Wu

Abstract

Suffix arrays and their variants are used widely for representing genomes in search applications. Enhanced suffix arrays (ESAs) provide fast search speed, but require large auxiliary data structures for storing longest common prefix and child interval information. We explore techniques for compressing ESAs to accelerate genomic search and reduce memory requirements. We evaluate various bitpacking techniques that store integers in fewer than 32 bits each, as well as bytecoding methods that reserve a single byte per integer whenever possible. Our results on the fly, chicken, and human genomes show that bytecoding with an exception guide array is the fastest method for retrieving auxiliary information. Genomic searching can be further accelerated using a data structure called a discriminating character array, which reduces memory accesses to the suffix array and the genome string. Finally, integrating storage of the auxiliary and discriminating character arrays further speeds up genomic search. The combination of exception guide arrays, a discriminating character array, and integrated data storage provide a 2- to 3-fold increase in speed for genomic searching compared with using bytecoding alone, and is 20 % faster and 40 % more space-efficient than an uncompressed ESA.

X Demographics

X Demographics

The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 13 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 13 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 3 23%
Researcher 3 23%
Professor 2 15%
Student > Master 2 15%
Student > Doctoral Student 1 8%
Other 1 8%
Unknown 1 8%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 4 31%
Computer Science 4 31%
Agricultural and Biological Sciences 2 15%
Unknown 3 23%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 26 April 2016.
All research outputs
#15,369,653
of 22,865,319 outputs
Outputs from Algorithms for Molecular Biology
#148
of 264 outputs
Outputs of similar age
#179,545
of 299,155 outputs
Outputs of similar age from Algorithms for Molecular Biology
#8
of 12 outputs
Altmetric has tracked 22,865,319 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 264 research outputs from this source. They receive a mean Attention Score of 3.2. This one is in the 34th percentile – i.e., 34% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 299,155 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 31st percentile – i.e., 31% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 12 others from the same source and published within six weeks on either side of this one. This one is in the 25th percentile – i.e., 25% of its contemporaries scored the same or lower than it.