Illinois Data Bank - Dataset

HIPPI Dataset
Cite this dataset:
Nguyen, Nam-phuong; Nute, Mike; Mirarab, Siavash; Warnow, Tandy (2016): HIPPI Dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6795126_V1
Dataset Description

This archive contains all the alignments and trees used in the HIPPI paper [1]. The pfam.tar archive contains the PFAM families
used to build the HMMs and BLAST databases. The file structure is:

./X/Y/initial.fasttree
./X/Y/initial.fasta

where X is a Pfam family, Y is the cross-fold set (0, 1, 2, or 3). Inside the folder
are two files, initial.fasta which is the Pfam reference alignment with 1/4 of the
seed alignment removed and initial.fasttree, the FastTree-2 ML tree estimated on
the initial.fasta.

The query.tar archive contains the query sequences for each cross-fold set.

The associated query sequences for a cross-fold Y is labeled as query.Y.Z.fas,
where Z is the fragment length (1, 0.5, or 0.25). The query files are found
in the splits directory.

[1] Nguyen, Nam-Phuong D, Mike Nute, Siavash Mirarab, and Tandy Warnow. (2016) HIPPI: Highly Accurate Protein Family Classification with Ensembles of HMMs. To appear in BMC Genomics.
Subject Life Sciences
Keywords HIPPI dataset; ensembles of profile Hidden Markov models; Pfam
License CC0
Funder U.S. National Science Foundation (NSF)-Grant:DBI-1461364
Funder U.S. National Science Foundation (NSF)-Grant:ABI-1458652
Funder U.S. National Science Foundation (NSF)-Grant:III:AF:1513629
Funder University of Illinois at Urbana-Champaign
Corresponding Creator Tandy Warnow
Downloaded 662 times
Version DOI Comment Publication Date
1 10.13012/B2IDB-6795126_V1 2016-08-16

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Creator create: {"family_name"=>"Warnow", "given_name"=>"Tandy", "identifier"=>"", "email"=>"warnow@illinois.edu", "is_contact"=>true, "row_position"=>4} 2016-08-26T15:00:54Z
Creator create: {"family_name"=>"Mirarab", "given_name"=>"Siavash", "identifier"=>"", "email"=>"smirarab@gmail.com", "is_contact"=>false, "row_position"=>3} 2016-08-26T15:00:54Z
Creator create: {"family_name"=>"Nute", "given_name"=>"Mike", "identifier"=>"", "email"=>"nute2@illinois.edu", "is_contact"=>false, "row_position"=>2} 2016-08-26T15:00:54Z
Creator update: {"is_contact"=>[true, false]} 2016-08-26T15:00:54Z
Dataset update: {"corresponding_creator_name"=>["Nam-phuong Nguyen", "Tandy Warnow"], "corresponding_creator_email"=>["namphuon@cs.utah.edu", "warnow@illinois.edu"]} 2016-08-26T15:00:54Z
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