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Visualizing the Protein Sequence Universe
Concurrency and computation, 2014-04, Vol.26 (6), p.1313-1325
Stanberry, Larissa
Higdon, Roger
Haynes, Winston
Kolker, Natali
Broomall, William
Ekanayake, Saliya
Hughes, Adam
Ruan, Yang
Qiu, Judy
Kolker, Eugene
Fox, Geoffrey
2014
Details
Autor(en) / Beteiligte
Stanberry, Larissa
Higdon, Roger
Haynes, Winston
Kolker, Natali
Broomall, William
Ekanayake, Saliya
Hughes, Adam
Ruan, Yang
Qiu, Judy
Kolker, Eugene
Fox, Geoffrey
Titel
Visualizing the Protein Sequence Universe
Ist Teil von
Concurrency and computation, 2014-04, Vol.26 (6), p.1313-1325
Ort / Verlag
Blackwell Publishing Ltd
Erscheinungsjahr
2014
Link zum Volltext
Quelle
Wiley Online Library
Beschreibungen/Notizen
SUMMARYModern biology is experiencing a rapid increase in data volumes that challenges our analytical skills and existing cyberinfrastructure. Exponential expansion of the protein sequence universe (PSU), the protein sequence space, together with the costs and complexities of manual curation creates a major bottleneck in life sciences research. Existing resources lack scalable visualization tools that are instrumental for functional annotation. Here, we describe a new visualization tool using multidimensional scaling to create a 3D embedding of the protein space. The advantages of the proposed PSU method include the ability to scale to large numbers of sequences, integrate different similarity measures with other functional and experimental data, and facilitate protein annotation. We applied the method to visualize the prokaryotic PSU using sequence alignment scores. As an annotation example, we used the interpolation approach to map the set of annotated archaeal proteins into the prokaryotic PSU. Transdisciplinary approaches akin to the one described in this paper are urgently needed to quickly and efficiently translate the influx of new data into tangible innovations and groundbreaking discoveries. Copyright © 2013 John Wiley & Sons, Ltd.
Sprache
Englisch
Identifikatoren
ISSN: 1532-0626
eISSN: 1532-0634
DOI: 10.1002/cpe.3072
Titel-ID: cdi_proquest_miscellaneous_1520965980
Format
–
Schlagworte
Annotations
,
Azure
,
BLAST
,
COG
,
computational bioinfor-matics
,
data visualization
,
data-enabled life sciences
,
DELSA
,
Hadoop
,
Hive
,
MapReduce
,
Mathematical analysis
,
MPI
,
multidimensional scaling
,
Needleman-Wunsch
,
protein annotation
,
protein sequence universe
,
Proteins
,
PSU
,
PSU, COG
,
Sammon
,
sequence similarity
,
Sequences
,
Similarity
,
Three dimensional
,
Twister
,
UniProt
,
UniRef
,
Universe
,
Visualization
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