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 |
| _version_ | 1797920103694598144 |
|---|---|
| author | Gıyasettin Özcan Burak Koca |
| author_facet | Gıyasettin Özcan Burak Koca |
| author_sort | Gıyasettin Özcan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-10T13:56:04Z |
| format | Article |
| id | doaj.art-f0a29512de12433bb89142ae9349bc2a |
| institution | Directory Open Access Journal |
| issn | 2148-4147 2148-4155 |
| language | English |
| last_indexed | 2024-04-10T13:56:04Z |
| publishDate | 2018-10-01 |
| publisher | Bursa Uludag University |
| record_format | Article |
| series | Uludağ University Journal of The Faculty of Engineering |
| spelling | doaj.art-f0a29512de12433bb89142ae9349bc2a2023-02-15T16:10:29ZengBursa Uludag UniversityUludağ University Journal of The Faculty of Engineering2148-41472148-41552018-10-012339110210.17482/uumfd.4250941779A New Automata Based Approximate String Matching Approach and Web Interface for Bioinformatics AlgorithmsGıyasettin Özcan0Burak Koca1ULUDAĞ ÜNİVERSİTESİ, MÜHENDİSLİK FAKÜLTESİGEBZE TEKNİK ÜNİVERSİTESİIn 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.https://dergipark.org.tr/tr/pub/uumfd/issue/39804/425094a-bombiyoinformatikara yüzyaklaşık desen eşleştirmebioinformaticsa-bominterfaceapproximate pattern matching |
| spellingShingle | Gıyasettin Özcan Burak Koca A New Automata Based Approximate String Matching Approach and Web Interface for Bioinformatics Algorithms Uludağ University Journal of The Faculty of Engineering a-bom biyoinformatik ara yüz yaklaşık desen eşleştirme bioinformatics a-bom interface approximate pattern matching |
| title | A New Automata Based Approximate String Matching Approach and Web Interface for Bioinformatics Algorithms |
| title_full | A New Automata Based Approximate String Matching Approach and Web Interface for Bioinformatics Algorithms |
| title_fullStr | A New Automata Based Approximate String Matching Approach and Web Interface for Bioinformatics Algorithms |
| title_full_unstemmed | A New Automata Based Approximate String Matching Approach and Web Interface for Bioinformatics Algorithms |
| title_short | A New Automata Based Approximate String Matching Approach and Web Interface for Bioinformatics Algorithms |
| title_sort | new automata based approximate string matching approach and web interface for bioinformatics algorithms |
| topic | a-bom biyoinformatik ara yüz yaklaşık desen eşleştirme bioinformatics a-bom interface approximate pattern matching |
| url | https://dergipark.org.tr/tr/pub/uumfd/issue/39804/425094 |
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