2015 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, 創薬基盤研究部門, 主任研究員 (40462832)
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| Project Period (FY) |
2014-04-01 – 2017-03-31
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| Keywords | バイオインフォマティクス / 生体情報学 / 比較ゲノム |
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| Outline of Annual Research Achievements |
The main achievement was publication of a paper in Genome Biology, describing a new computational method to align orthologous regions of two genomes more accurately than before. In particular, the method finds rearrangements, such as inversions and translocations, very accurately. Actually, this method is not specific to whole-genome comparison: it works just as well for finding rearrangements in DNA reads versus a reference genome. This is especially relevant to recent long DNA reads, such as those from PacBio and nanopore: their length and high error rate makes their alignment resemble genome
comparison.
With my collaborators in NCBI (USA), I published a paper describing a software library for calculating the statistical significance of pair-wise alignments. Its useful feature is that it allows us to use new alignment parameters, fitted to the rates of substitution, insertion, and deletion, in any data. This should help us to find related sequence regions more accurately.
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| Current Status of Research Progress |
Current Status of Research Progress
3: Progress in research has been slightly delayed.
Reason
I hired a foreign postdoctoral fellow in 2015. Unfortunately, he quit after a few weeks, because he found the salary too low compared to the cost of living in Tokyo. The failure to hire someone obviously delays the project. Nevertheless, there were good achievements during the year, described above.
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| Strategy for Future Research Activity |
I have hired a new postdoctoral fellow, who will start this summer. Although she is also foreign, she has already visited me for 3 days (unlike the previous person), so she has a better idea of the circumstances. We also managed to arrange a higher salary for her.
We will use our computational methods developed so far, to look for related regulatory sequences in distantly-related genomes. An unexpected development is that our methods are especially good for detecting rearrangements. So we would like to thoroughly survey rearrangments in genome evolution, which has never been done before. Previous studies have thoroughly looked at only the simplest rearrangements, in particular inversions. Little is known about what types of more complex rearrangement exist.
To carry out this research, we plan to buy new computer hardware. We will also travel to conferences, to disseminate our results to the research community, and seek opportunities to synergize with other researchers.
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| Causes of Carryover |
The main reason is to employ a postdoctoral fellow to help perform the research. We also wish to buy computer hardware, with large memory and many processors, which is necessary for exquisite comparison of large genome sequences, and also for comparing them to databases of known functional sequence, such as proteins. We will also travel to conferences, to disseminate our results to the research community, and seek opportunities to synergize with other researchers. Finally, we will likely need to pay to publish our results in open-access journals.
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| Expenditure Plan for Carryover Budget |
The funding will be used to hire one postdoctoral fellow, who has already accepted our job offer. We will then buy computer hardware with large memory and multi-processors, as well as a laptop and standard office software for the new postdoc. We will both travel to at least one international and two domestic conferences, one of which is WABI (Workshop on Algorithms in Bioinformatics) 2016 in Denmark, which I am co-organizing. Finally, we will pay to publish our results in open-access journals.
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