• Shigehiro Kuraku




突然失礼いたします。来週水曜30日の14時より、私の神戸理研のラボのメンバーであるJohn Rozewickiさんの進捗レポートを行います。アラインメントビューワー開発やゲノムブラウザJBrowse2の利用を中心とした、技術開発の話題を扱います。もしご興味おありでしたら気軽にご参加ください。また、このアナウンスは研究室内でご転送いただいて構いません。

 本来は内輪で行うような会ではありますが、広く知っていただくことにより価値があると思い、あえてご連絡差し上げました。ちなみに、 アラインメントビューワーの開発については、アラインメントプログラムMAFFT開発の一部として、昨年12月の分子生物学会にて発表しています(発表ムービー)。下記にその要旨を貼り付けておきます。

Title: Efficient visualization of large-scale sequence alignments in the web browser

Presenters: John Rozewicki, Shigehiro Kuraku, Kazutaka Katoh

Abstract: The amount of sequence data available to researchers increases every year. Developers of sequence alignment tools such as MAFFT have worked hard to handle this large-scale data with many thousands of sequences and many thousands of sites by developing new algorithms and reimplementing older algorithms to take advantage of resources like cloud computing. A frequent use case in recent years has been the direct comparison of SARS- CoV-2 genomes. Manual inspection of alignment results can help to avoid misapplication of alignment methods and overlooking obvious observations. However, solutions for viewing and interpreting sequence alignments have not kept pace with the growth in data. Most were built in a time when sequence alignment results tended to be much smaller. When trying to view large-scale sequence alignments in existing solutions they often crash, are extremely slow, or fail to give a useful overview of data. This presentation will describe the design and features of a new web browser-based sequence alignment viewer built with WebAssembly/WebGL/HTML5 by the MAFFT team, from the ground up, for large-scale data. A key focus of the presentation will be efficient techniques for visualization of large-scale data which may be applicable to other areas beyond sequence alignment visualization. This new viewer has been tested on sequence alignments larger than 500 million letters (=100,000 sequences x 5000 sites or 100 sequences x 5 million sites), and performs smoothly even on inexpensive systems. Moreover, because it is built using widely compatible web technologies it is able to run not only on full computers, but also on handheld devices such as phones and tablets.