NDLI: Potential Perils of Biological Sequence Visualization Using Sequence Logo

Content Provider	IEEE Xplore Digital Library
Author	Lee Nung Kion Oon Yin Bee
Copyright Year	2013
Description	Author affiliation: Fac. of Cognitive Sci. & Human Dev., Univ. Malaysia Sarawak, Kota Samarahan, Malaysia (Lee Nung Kion; Oon Yin Bee)
Abstract	Sequence motif's characteristics are commonly visualized by using a sequence logo. This paper describes a user study aimed at evaluating the effectiveness of sequence logo as evaluation metric for motif prediction tools. We also investigate the nature of confirmation biases in using sequence logos in result reporting in publications. While sequence logos have been widely used for visualizing sequence motifs in the past 20 years, no study has reported its effectiveness and possible misuses in decision making. We conducted a paper-and-pencil test to determine the effectiveness of sequence logos in some of their common usages. A survey study was also performed to investigate sequence logos' learn ability. We found that there are great mismatches between users' perception and actual quality of motifs when sequence logos were used as an evaluation metric. Therefore, evaluation of motif prediction tools based on sequence logos has to be interpreted cautiously. Our result also suggests that there are still room for improvements in the current sequence logo's layout design.
Starting Page	106
Ending Page	111
File Size	220871
Page Count	6
File Format	PDF
ISBN	9780769550510
DOI	10.1109/CGIV.2013.26
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-08-06
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Measurement Proteins Visualization sequence logo Decision making DNA motif visualization Color Usability confirmation bias
Content Type	Text
Resource Type	Article

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