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Development of an integrated suite of software in analysing of large DNA databases.

Kong KS, Ng EY - Open Med Inform J (2008)

Bottom Line: The integrated software tool has great potential and that the results obtained during the tests were satisfactory.The recent South Asia Tsunami incident has renewed the need to establish a quick and reliable system for DNA matching and comparison.Fault tolerance enhancement to the system is one of the key areas that can further help to make the entire application efficient, robust and reliable.

View Article: PubMed Central - PubMed

Affiliation: DS Center/IEP, DSO National Laboratories, 20 Science Park Drive, Singapore 118230.

ABSTRACT
The work showed that the integrated suite of software tools for detecting criminals using DNA databases has achieved the overall objective by providing a working platform for sequence analysis. The work also demonstrated that by integrating BLAST and FASTA (two widely used and freely available algorithms), plus an additional implementation of PSA (custom-built pairwise sequence alignment algorithms) and TR analysis tools (for detecting tandem repeats) with the rest of the utilities supporting tools (databases and files management) developed, it is entirely possible to have an initial working version of the software tool for criminal DNA analysis and detection work. The integrated software tool has great potential and that the results obtained during the tests were satisfactory. The recent South Asia Tsunami incident has renewed the need to establish a quick and reliable system for DNA matching and comparison. This work may also contribute towards the quick identification of victims in many disasters.Future works are to further enhance the existing tools by adding more options and controls, improve upon the visualisation display, and to build robust software architecture to better manage the system loadings. Fault tolerance enhancement to the system is one of the key areas that can further help to make the entire application efficient, robust and reliable.

No MeSH data available.


System Architecture.
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Figure 7: System Architecture.

Mentions: Fig. (7) depicts the high-level system architecture of the system developed. The user interacts with the system via a GUI (Graphical User Interface) display to perform sequence alignment operations. The sequence alignment algorithms included in this work are PSA, BLAST, FASTA and Dotplot. In addition, TR is used for tandem repeats analysis. PSA, TR and Dotplot are custom-built applications using the Java SDK, whereas BLAST and FASTA are both open-source applications freely available for development use and have been integrated to the system. The rest are utilities developed to support Sequence Analysis Work. Examples are a set of database utilities for index (key) creation, data conversion, and packaging of data into the Fasta data format (i.e. BlastFastaData) for database search, which are particularly used by BLAST and FASTA algorithms. Also, BioJava utilities for creating and maintaining data (i.e. BioData) that is compatible to BioJava standard, are used by the PSA algorithm. BioJava also provides many other sequence routines, algorithms and libraries for building bio-applications. In addition, a text file editor is also developed to facilitate sequence files editing.


Development of an integrated suite of software in analysing of large DNA databases.

Kong KS, Ng EY - Open Med Inform J (2008)

System Architecture.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666961&req=5

Figure 7: System Architecture.
Mentions: Fig. (7) depicts the high-level system architecture of the system developed. The user interacts with the system via a GUI (Graphical User Interface) display to perform sequence alignment operations. The sequence alignment algorithms included in this work are PSA, BLAST, FASTA and Dotplot. In addition, TR is used for tandem repeats analysis. PSA, TR and Dotplot are custom-built applications using the Java SDK, whereas BLAST and FASTA are both open-source applications freely available for development use and have been integrated to the system. The rest are utilities developed to support Sequence Analysis Work. Examples are a set of database utilities for index (key) creation, data conversion, and packaging of data into the Fasta data format (i.e. BlastFastaData) for database search, which are particularly used by BLAST and FASTA algorithms. Also, BioJava utilities for creating and maintaining data (i.e. BioData) that is compatible to BioJava standard, are used by the PSA algorithm. BioJava also provides many other sequence routines, algorithms and libraries for building bio-applications. In addition, a text file editor is also developed to facilitate sequence files editing.

Bottom Line: The integrated software tool has great potential and that the results obtained during the tests were satisfactory.The recent South Asia Tsunami incident has renewed the need to establish a quick and reliable system for DNA matching and comparison.Fault tolerance enhancement to the system is one of the key areas that can further help to make the entire application efficient, robust and reliable.

View Article: PubMed Central - PubMed

Affiliation: DS Center/IEP, DSO National Laboratories, 20 Science Park Drive, Singapore 118230.

ABSTRACT
The work showed that the integrated suite of software tools for detecting criminals using DNA databases has achieved the overall objective by providing a working platform for sequence analysis. The work also demonstrated that by integrating BLAST and FASTA (two widely used and freely available algorithms), plus an additional implementation of PSA (custom-built pairwise sequence alignment algorithms) and TR analysis tools (for detecting tandem repeats) with the rest of the utilities supporting tools (databases and files management) developed, it is entirely possible to have an initial working version of the software tool for criminal DNA analysis and detection work. The integrated software tool has great potential and that the results obtained during the tests were satisfactory. The recent South Asia Tsunami incident has renewed the need to establish a quick and reliable system for DNA matching and comparison. This work may also contribute towards the quick identification of victims in many disasters.Future works are to further enhance the existing tools by adding more options and controls, improve upon the visualisation display, and to build robust software architecture to better manage the system loadings. Fault tolerance enhancement to the system is one of the key areas that can further help to make the entire application efficient, robust and reliable.

No MeSH data available.