Software

SPADE

github

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.

Mori H, Evans-Yamamoto D, Ishiguro S, Tomita M & Yachie N. Fast and global detection of periodic sequence repeats in large genomic resources. (2019) Nucleic Acids Research 47, e8 PubMed PDF

Base editing prediction model

github

A Python script used for the base editing prediction in the following paper.

Sakata RC+, Ishiguro S+, Mori H+, 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. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. (2020) Nature Biotechnology 38, 865-869 PubMed PDF Addgene
+Equally contributed

FRACTAL

github

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.

Konno N, Kijima Y, Watano K, Ishiguro S, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W & Yachie N. Deep distributed computing to reconstruct extremely large lineage trees. (2022) Nature Biotechnology 40, 566–575 PubMed PDF Supplementary Materials GIFtorial

PRESUME

github

PRESUME is a software tool that simulates cell division or speciation and diversification of DNA sequences in the growing population.

Konno N, Kijima Y, Watano K, Ishiguro S, Ono K, Tanaka M, Mori H, Masuyama N, Pratt D, Ideker T, Iwasaki W & Yachie N. Deep distributed computing to reconstruct extremely large lineage trees. (2022) Nature Biotechnology 40, 566–575 PubMed PDF Supplementary Materials GIFtorial

QUEEN

github

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.

Mori H & Yachie N. A universal framework to efficiently share material and process resources in the DNA construction world. arXiv 2111.15175

INTERSTELLAR

github

INTERSTELLAR (interpretation, scalable transformation, and emulation of large-scale sequencing reads) is a versatile software tool that interprets data values encoded in sequencing reads and translates them into sequencing reads of another structure according to a user-defined process configuration file. For example, sci-RNA-seq3 reads can be analyzed using dropseq-tools and Slide-seq reads can be analyzed by Space Ranger. Value space can be optimized even when the information representability of source reads is higher than that of destination reads. Various error correction choices are available. INTERSTELLAR is compatible with distributed computing environments.

Kijima Y, Evans-Yamamoto D, Toyoshima H & Yachie N. A universal sequencing read interpreter. bioRxiv 2022.04.16.488535