A basic analysis toolkit for biological sequences
<p>Abstract</p> <p>This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2007-09-01
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| Series: | Algorithms for Molecular Biology |
| Online Access: | http://www.almob.org/content/2/1/10 |
| _version_ | 1811320753279205376 |
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| author | Siragusa Enrico Siragusa Alessandro Giancarlo Raffaele Utro Filippo |
| author_facet | Siragusa Enrico Siragusa Alessandro Giancarlo Raffaele Utro Filippo |
| author_sort | Siragusa Enrico |
| collection | DOAJ |
| description | <p>Abstract</p> <p>This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at <url>http://www.math.unipa.it/~raffaele/BATS/</url> under the GNU GPL.</p> |
| first_indexed | 2024-04-13T13:06:01Z |
| format | Article |
| id | doaj.art-357238b89cf84e8e92ac03c21cb9e50a |
| institution | Directory Open Access Journal |
| issn | 1748-7188 |
| language | English |
| last_indexed | 2024-04-13T13:06:01Z |
| publishDate | 2007-09-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj.art-357238b89cf84e8e92ac03c21cb9e50a2022-12-22T02:45:47ZengBMCAlgorithms for Molecular Biology1748-71882007-09-01211010.1186/1748-7188-2-10A basic analysis toolkit for biological sequencesSiragusa EnricoSiragusa AlessandroGiancarlo RaffaeleUtro Filippo<p>Abstract</p> <p>This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at <url>http://www.math.unipa.it/~raffaele/BATS/</url> under the GNU GPL.</p>http://www.almob.org/content/2/1/10 |
| spellingShingle | Siragusa Enrico Siragusa Alessandro Giancarlo Raffaele Utro Filippo A basic analysis toolkit for biological sequences Algorithms for Molecular Biology |
| title | A basic analysis toolkit for biological sequences |
| title_full | A basic analysis toolkit for biological sequences |
| title_fullStr | A basic analysis toolkit for biological sequences |
| title_full_unstemmed | A basic analysis toolkit for biological sequences |
| title_short | A basic analysis toolkit for biological sequences |
| title_sort | basic analysis toolkit for biological sequences |
| url | http://www.almob.org/content/2/1/10 |
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