2016 Fiscal Year Annual Research Report
Regulatory DNA conserved between Phyla
| Project/Area Number |
26700030
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| Research Institution | National Institute of Advanced Industrial Science and Technology |
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Principal Investigator |
Frith Martin 国立研究開発法人産業技術総合研究所, 人工知能研究センター, 上級主任研究員 (40462832)
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| Project Period (FY) |
2014-04-01 – 2018-03-31
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| Keywords | orthology / alignment / probability / substitution / insertion / deletion |
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| Outline of Annual Research Achievements |
The main research achievement was to develop and publish a very useful piece of software: "last-train". This software is given two sets of DNA sequences (e.g. two genomes). It determines the frequencies of insertions, deletions, and each kind of substitution (e.g. a->g) between orthologous regions of these sequences. Once we know these frequencies, we can compare and align the sequences more accurately. This has quite wide applications: not only to comparing two genomes, but also to aligning DNA reads to a genome. This software was published as: "Training alignment parameters for arbitrary sequencers with LAST-TRAIN" Bioinformatics. 2017 Mar 15;33(6):926-928.
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| Current Status of Research Progress |
Current Status of Research Progress
3: Progress in research has been slightly delayed.
Reason
I have found it difficult to recruit a postdoctoral researcher. I recruited one researcher last year, who quit after a few weeks. I recruited another this year, who was very promising, but had to suddenly change affiliations for critical career reasons.
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| Strategy for Future Research Activity |
A development that was not initially planned is that our methods seem uniquely good for characterizing rearrangements in genome evolution (and disease). Therefore, this opportunity should be taken to explore what kinds of rearrangements occur, and what effect they have (e.g. on gene structure). It seems that specific, and perhaps unexpected patterns of rearrangement seem to frequently recur, such as a small invertion adjacent to a large deletion.
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| Causes of Carryover |
The reasons for not spending some of the budget last year, and for spending this year, are as follows. The spending last year was reduced, because a postdoc was employed for this project for only some months, less than the whole year. The aim in the coming year is to obtain some biological results, using the computational methods developed so far. Also, it is important at this stage to disseminate the results by publishing and presenting at meetings.
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| Expenditure Plan for Carryover Budget |
The usage plan is as follows. The funding will be used to pay for software development work, to further develop our computational tools and ready them for easy practical use. Also, computer hardware will be purchased to apply the methods comprehensively to public genomic datasets. The funding will be used to attend at least one international and one domestic conference, and to pay (open-access) publication costs for journal publication.
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