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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.


TR search tool parameters.
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Figure 14: TR search tool parameters.

Mentions: The inputs to TR search tool are: (1) suspect’s DNA sequence; and (2) minimum and maximum TR word size. During stage 1, the suspect’s DNA sequence is analysed and the TR tool will locate all possible ETRs found within the nucleotide sequence based on the selected TR word size. The tool allows the TR word size to be configured freely, as well as to shorten or widen the sliding window size (the sliding window is used to scan along the sequence and to locate possible TRs). Once all the possible TRs are identified, the user is able to select one or more TRs to scan the selected databases for a possible match. If one or more matches are found, the results are displayed on the MMI. See Fig. (14).


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

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

TR search tool parameters.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 14: TR search tool parameters.
Mentions: The inputs to TR search tool are: (1) suspect’s DNA sequence; and (2) minimum and maximum TR word size. During stage 1, the suspect’s DNA sequence is analysed and the TR tool will locate all possible ETRs found within the nucleotide sequence based on the selected TR word size. The tool allows the TR word size to be configured freely, as well as to shorten or widen the sliding window size (the sliding window is used to scan along the sequence and to locate possible TRs). Once all the possible TRs are identified, the user is able to select one or more TRs to scan the selected databases for a possible match. If one or more matches are found, the results are displayed on the MMI. See Fig. (14).

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.