Potential Perils of Biological Sequence Visualization using Sequence Logo
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...
| Main Authors: | , |
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| Format: | Proceeding |
| Language: | English |
| Published: |
2013
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| Subjects: | |
| Online Access: | http://ir.unimas.my/id/eprint/11931/ http://ir.unimas.my/id/eprint/11931/1/Potential%20Perils_abstract.pdf |
| _version_ | 1848837091480305664 |
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| author | Lee, Nung Kion Oon, Yin Bee |
| author_facet | Lee, Nung Kion Oon, Yin Bee |
| author_sort | Lee, Nung Kion |
| building | UNIMAS Institutional Repository |
| collection | Online Access |
| description | 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’ learnability. 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. |
| first_indexed | 2025-11-15T06:34:09Z |
| format | Proceeding |
| id | unimas-11931 |
| institution | Universiti Malaysia Sarawak |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T06:34:09Z |
| publishDate | 2013 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | unimas-119312016-05-12T04:33:14Z http://ir.unimas.my/id/eprint/11931/ Potential Perils of Biological Sequence Visualization using Sequence Logo Lee, Nung Kion Oon, Yin Bee Q Science (General) QA Mathematics 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’ learnability. 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. 2013 Proceeding NonPeerReviewed text en http://ir.unimas.my/id/eprint/11931/1/Potential%20Perils_abstract.pdf Lee, Nung Kion and Oon, Yin Bee (2013) Potential Perils of Biological Sequence Visualization using Sequence Logo. In: Computer Graphics, Imaging and Visualization (CGIV), 2013 10th International Conference, 6-8 Aug. 2013, Macau. http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6658172 10.1109/CGIV.2013.26 |
| spellingShingle | Q Science (General) QA Mathematics Lee, Nung Kion Oon, Yin Bee Potential Perils of Biological Sequence Visualization using Sequence Logo |
| title | Potential Perils of Biological Sequence Visualization using Sequence Logo |
| title_full | Potential Perils of Biological Sequence Visualization using Sequence Logo |
| title_fullStr | Potential Perils of Biological Sequence Visualization using Sequence Logo |
| title_full_unstemmed | Potential Perils of Biological Sequence Visualization using Sequence Logo |
| title_short | Potential Perils of Biological Sequence Visualization using Sequence Logo |
| title_sort | potential perils of biological sequence visualization using sequence logo |
| topic | Q Science (General) QA Mathematics |
| url | http://ir.unimas.my/id/eprint/11931/ http://ir.unimas.my/id/eprint/11931/ http://ir.unimas.my/id/eprint/11931/ http://ir.unimas.my/id/eprint/11931/1/Potential%20Perils_abstract.pdf |