2014 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, ゲノム情報研究センター, 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 |
In this first year, groundwork for the project was laid. I improved computational methods to accurately compare and align genome sequences, in particular, taking careful account of rearrangements, such as inversions and translocations. I also improved methods to compare genomic DNA to protein sequence databases, which is important for annotating genomic elements.
I also began a collaboration with Drs. Y Suzuki (Tokyo University) and W Makalowski (Muenster University) on analyzing DNA sequence data obtained with the new "nanopore" sequencing technique. This is a promising way to obtain new genomic sequence: it is cheap, fast, and produces long reads, but at present it has a very high error rate. Comparing high-error sequences is quite similar to comparing distantly-related genomes.
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| Current Status of Research Progress |
Current Status of Research Progress
4: Progress in research has been delayed.
Reason
I aim to hire a postdoctoral fellow to assist with this project.
Since this is my first ever funding, I could not start to advertise for a postdoctoral position until I knew that I would receive the funding. This year, I began the process of interviewing several candidates. The project can proceed more quickly once someone is hired to work on it.
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| Strategy for Future Research Activity |
In the second year, we will finalize and publish the improved computational methods developed in the first year. We will also apply them to compare the human genome to genomes of various other species.
We will also work on training alignment parameters. Distantly-related DNA sequences have certain frequencies of substitutions, insertions, and deletions: we will learn these from the data, so that we can then align such sequences more accurately. We have started doing this for nanopore DNA sequences, but the aim is to develop a general method that works for all kinds of DNA data. Since different kinds of DNA (e.g. protein-coding versus non-coding) will differ in these parameters, the training will have to be done in a careful way: separately for these different kinds of DNA (the main interest of this project being non-protein-coding DNA.)
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| Causes of Carryover |
The main cost is to hire a postdoctoral fellow, to help do the work of this project. We also need to travel, to attend conferences and meet other researchers in related fields: our research will become more powerful and useful if we can collaborate with complementary researchers, such as those sequencing new genomes. Finally, since our project uses computers for deep analysis of large genomic datasets, we need powerful computer hardware.
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| Expenditure Plan for Carryover Budget |
The funding will be used to hire one postdoctoral fellow, and purchase startup equipment for him/her (a capable computer and standard office software). We will then attend several international and domestic conferences, including the 29th International Mammalian Genome Conference, and the Genome Informatics Workshop. Also, we will need to pay to publish our results in open-access journals.
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Research Products
(2 results)
