The 16S.B.ALL dataset in 100-HF condition
Citation:
Shen, Chengze; Park, Minhyuk; Warnow, Tandy (2022): The 16S.B.ALL dataset in 100-HF condition. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6604429_V1
Persistent link for this dataset:
Dataset Description

This upload includes the 16S.B.ALL in 100-HF condition (referred to as 16S.B.ALL-100-HF) used in Experiment 3 of the WITCH paper (currently accepted in principle by the Journal of Computational Biology). 100-HF condition refers to making sequences fragmentary with an average length of 100 bp and a standard deviation of 60 bp. Additionally, we enforced that all fragmentary sequences to have lengths > 50 bp. Thus, the final average length of the fragments is slightly higher than 100 bp (~120 bp).

In this case (i.e., 16S.B.ALL-100-HF), 1,000 sequences with lengths 25% around the median length are retained as "backbone sequences", while the remaining sequences are considered "query sequences" and made fragmentary using the "100-HF" procedure. Backbone sequences are aligned using MAGUS (or we extract their reference alignment). Then, the fragmentary versions of the query sequences are added back to the backbone alignment using either MAGUS+UPP or WITCH.

More details of the tar.gz file are described in README.txt.
Subject Technology and Engineering
Keywords MAGUS;UPP;Multiple Sequence Alignment;eHMMs
License CC0
Funder U.S. National Science Foundation (NSF) - Grant: 2006069
Corresponding Creator Chengze Shen
Downloaded 148 times

Related Materials:
   Article Shen, Chengze, Minhyuk Park, and Tandy Warnow. 2022. “WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment.” Journal of Computational Biology : A Journal of Computational Molecular Cell Biology, May. doi:10.1089/cmb.2021.0585.
Version DOI Comment Publication Date
1 10.13012/B2IDB-6604429_V1 2022-03-25
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update: {"version_comment"=>[nil, ""], "subject"=>[nil, "Life Sciences"]} 2022-03-28T21:02:15Z