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<section class="posts"><h1 class="page_title All Common" id="software">Software</h1><h2 class="page_title All Common">INTERSTELLAR</h2><section class="content All Common" id="">
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<section class="content All Common" id="">
<p><a href="https://github.com/yachielab/Interstellar">github</a></p>
<p>INTERSTELLAR (interpretation, scalable transformation, and emulation of large-scale sequencing reads) is a versatile software tool that extracts data values from sequencing reads and translates them into sequencing reads of another structure according to a user-defined process configuration file.</p>
</section>
<section class="paper All Common" id="">
<section class="paper_txt_wo_photo"><p class="author">Kijima Y, Evans-Yamamoto D, Toyoshima H & <span class="member">Yachie N</span></p>
<p class="title">A universal sequencing read interpreter.</p>
<p class="info"><a class="JT" href="https://www.science.org/doi/full/10.1126/sciadv.add2793?rfr_dat=cr_pub++0pubmed&url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org">Science Advances</a> 9, eadd2793, 2023 <a class="PMID" href="https://pubmed.ncbi.nlm.nih.gov/36598975/">PubMed</a></p>
</section>
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<h2 class="page_title All Common">QUEEN</h2><section class="content All Common" id="">
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<p><a href="https://github.com/yachielab/QUEEN">github</a></p>
<p>QUEEN is a framework to generate quinable and efficiently editable nucleotide sequence resources to resolve many current issues in building DNA. QUEEN enables to design a new DNA by using existing DNA resource files and records the construction process in an output file (GenBank file format). The GenBank files generated by QUEEN are able to regenerate the process codes that perfectly clone themselves and bequeath the design history to successive DNA constructs that recycle their partial resources. QUEEN-generated GenBank files are compatible with the existing DNA repository services and software.</p>
</section>
<section class="paper All Common" id="">
<section class="paper_txt_wo_photo"><p class="author"><span class="member">Mori H</span> & <span class="member">Yachie N</span></p>
<p class="title">A framework to efficiently describe and share reproducible DNA materials and construction protocols.</p>
<p class="info"><a class="JT" href="https://www.nature.com/articles/s41467-022-30588-x">Nature Communications</a> 13, 2894, 2022 <a class="PMID" href="https://pubmed.ncbi.nlm.nih.gov/35610233/">PubMed</a> <a class="pdf-link" href="./pdf/s41467-022-30588-x.pdf">PDF</a></p>
</section>
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<h2 class="page_title All Common">FRACTAL</h2><section class="content All Common" id="">
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<section class="content All Common" id="">
<p><a href="https://github.com/yachielab/FRACTAL">github</a></p>
<p>FRACTAL (framework for distributed computing to trace huge accurate lineage) is a new distributed computing framework that is designated to reconstruct a large lineage of DNA sequences that have evolved or diversified from an ancestral DNA sequence through the accumulation of mutations.</p>
</section>
<section class="paper All Common" id="">
<section class="paper_txt_wo_photo"><p class="author">Konno N, <span class="member">Kijima Y</span>, <span class="member">Watano K</span>, <span class="member">Ishiguro S</span>, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W & Yachie N</p>
<p class="title">Deep distributed computing to reconstruct extremely large lineage trees.</p>
<p class="info"><a class="JT" href="https://www.nature.com/articles/s41587-021-01111-2">Nature Biotechnology</a> 40, 566-575, 2022 <a class="PMID" href="https://pubmed.ncbi.nlm.nih.gov/34992246/">PubMed</a></p>
</section>
</section>
<h2 class="page_title All Common">PRESUME</h2><section class="content All Common" id="">
<img src="./img/github_PRESUME.jpg" alt="content_img" style="width: clamp(250px, 80%, 600px);float: left; margin-left: 0;" class="content_img">
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<section class="content All Common" id="">
<p><a href="https://github.com/yachielab/PRESUME">github</a></p>
<p>PRESUME is a software tool that simulates cell division or speciation and diversification of DNA sequences in the growing population.</p>
</section>
<section class="paper All Common" id="">
<section class="paper_txt_wo_photo"><p class="author">Konno N, <span class="member">Kijima Y</span>, <span class="member">Watano K</span>, <span class="member">Ishiguro S</span>, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W & Yachie N</p>
<p class="title">Deep distributed computing to reconstruct extremely large lineage trees.</p>
<p class="info"><a class="JT" href="https://www.nature.com/articles/s41587-021-01111-2">Nature Biotechnology</a> 40, 566-575, 2022 <a class="PMID" href="https://pubmed.ncbi.nlm.nih.gov/34992246/">PubMed</a></p>
</section>
</section>
<h2 class="page_title All Common">Base editing prediction model</h2><section class="content All Common" id="">
<p><a href="https://github.com/yachielab/base-editing-prediction">github</a></p>
<p>A Python script used for the base editing prediction in the following paper.</p>
</section>
<section class="paper All Common" id="">
<section class="paper_txt_wo_photo"><p class="author"><span class="member">Sakata RC</span>, <span class="member">Ishiguro S</span>, <span class="member">Mori H</span>, Tanaka M, Tatsuno K, Ueda H, Yamamoto S, Seki M, Masuyama N, Nishida K, Nishimasu H, Arakawa K, Kondo A, Nureki O, Tomita M, Aburatani H & Yachie N</p>
<p class="title">Base editors for simultaneous introduction of C-to-T and A-to-G mutations.</p>
<p class="info"><a class="JT" href="https://www.nature.com/articles/s41587-020-0509-0">Nature Biotechnology</a> 38, 865-869, 2020 <a class="PMID" href="https://pubmed.ncbi.nlm.nih.gov/32483365/">PubMed</a> <a class="pdf-link" href="./pdf/s41587-020-0509-0.pdf">PDF</a></p>
</section>
</section>
<h2 class="page_title All Common">SPADE</h2><section class="content All Common" id="">
<p><a href="https://github.com/yachielab/SPADE">github</a></p>
<p>SPADE is a software tool to explore various periodic repeat regions from large genomic and protein data resources in a high-throughput and unsupervised manner.</p>
</section>
<section class="paper All Common" id="">
<section class="paper_txt_wo_photo"><p class="author"><span class="member">Mori H</span>, Evans-Yamamoto D, Ishiguro S, Tomita M & <span class="member">Yachie N</span></p>
<p class="title">Fast and global detection of periodic sequence repeats in large genomic resources.</p>
<p class="info"><a class="JT" href="https://academic.oup.com/nar/article/47/2/e8/5124599">Nucleic Acids Research</a> 47, e8, 2019 <a class="PMID" href="https://pubmed.ncbi.nlm.nih.gov/30304510/">PubMed</a> <a class="pdf-link" href="./pdf/gky890.pdf">PDF</a></p>
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