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A basic analysis toolkit for biological sequences.

Giancarlo R, Siragusa A, Siragusa E, Utro F - Algorithms Mol Biol (2007)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Matematica Applicazioni, Università di Palermo, Italy. raffaele@math.unipa.it

ABSTRACT
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 http://www.math.unipa.it/~raffaele/BATS/ under the GNU GPL.

No MeSH data available.


a snapshot of the GUI. An overview of the GUI of BATS. The top bar has a specific button for each of the algorithms and functions implemented. Then, each function has its own parameter selection interface. The Edit Distance function interface is shown here.
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Figure 1: a snapshot of the GUI. An overview of the GUI of BATS. The top bar has a specific button for each of the algorithms and functions implemented. Then, each function has its own parameter selection interface. The Edit Distance function interface is shown here.

Mentions: Here we concentrate on alignment problems involving only two sequences. In general, they can be divided in two areas: local and global alignments [1]. Local alignment methods try to find regions of high similarity between two strings, e.g. BLAST [5], as opposed to global alignment methods that assess an overall structural similarity between the two strings, e.g. the Gotoh alignment algorithm [6]. However, at the algorithmic level, both classes often share the same ideas and techniques, being in most cases all based on dynamic programming algorithms and related speed-ups [7]. More in detail, we have implementations for (see also Fig. 1 for the corresponding function in the GUI):


A basic analysis toolkit for biological sequences.

Giancarlo R, Siragusa A, Siragusa E, Utro F - Algorithms Mol Biol (2007)

a snapshot of the GUI. An overview of the GUI of BATS. The top bar has a specific button for each of the algorithms and functions implemented. Then, each function has its own parameter selection interface. The Edit Distance function interface is shown here.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2147010&req=5

Figure 1: a snapshot of the GUI. An overview of the GUI of BATS. The top bar has a specific button for each of the algorithms and functions implemented. Then, each function has its own parameter selection interface. The Edit Distance function interface is shown here.
Mentions: Here we concentrate on alignment problems involving only two sequences. In general, they can be divided in two areas: local and global alignments [1]. Local alignment methods try to find regions of high similarity between two strings, e.g. BLAST [5], as opposed to global alignment methods that assess an overall structural similarity between the two strings, e.g. the Gotoh alignment algorithm [6]. However, at the algorithmic level, both classes often share the same ideas and techniques, being in most cases all based on dynamic programming algorithms and related speed-ups [7]. More in detail, we have implementations for (see also Fig. 1 for the corresponding function in the GUI):

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dipartimento di Matematica Applicazioni, Università di Palermo, Italy. raffaele@math.unipa.it

ABSTRACT
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 http://www.math.unipa.it/~raffaele/BATS/ under the GNU GPL.

No MeSH data available.