A New Automata Based Approximate String Matching Approach and Web Interface for Bioinformatics Algorithms
In this study, we present a new web interface for major bioinformatics algorithms and introduce a novel approximate string matching algorithm. Our web interface executes major algorithms on the field for the use of computational biologists, students or any other interested researchers. In the web in...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Bursa Uludag University
2018-10-01
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| Series: | Uludağ University Journal of The Faculty of Engineering |
| Subjects: | |
| Online Access: | https://dergipark.org.tr/tr/pub/uumfd/issue/39804/425094 |
| Summary: | In
this study, we present a new web interface for major bioinformatics algorithms and
introduce a novel approximate string matching algorithm. Our web interface executes
major algorithms on the field for the use of computational biologists, students
or any other interested researchers. In the web interface, algorithms come
under three sections: Sequence alignment, pattern matching and motif finding. In
each section, we introduce algorithms in order to find best fitting one for
specific dataset and problem. The interface introduces execution time, memory
usage and context specific results of algorithms such as alignment score. The
interface utilizes emerging open source languages and tools. In order to
develop light and user-friendly interface, all parts of the interface coded
with Python language. On the other hand, Django is used for web interface. Second
contribution of the study is novel A-BOM algorithm, which is designed for
approximate pattern matching problem. The algorithm is approximate matching variation
of Backward Oracle Matching. We compare our algorithm with popular approximate
string matching algorithms. Results denote that A-BOM introduces %30 to %80 short
runtime improvement when compared to current approximate pattern matching algorithms
on long patterns. |
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| ISSN: | 2148-4147 2148-4155 |