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FlowerPower specifications

Information


Unique identifier OMICS_13087
Name FlowerPower
Interface Web user interface
Restrictions to use None
Input data A seed sequence, a specified database from which putative homologs will be selected, and user-selected alignment quality control criteria (coverage and percent identity cutoffs)
Output data Subfamily-HMM based alignment and a realignment of the sequences, functional subfamily, subfamily HMMs
Programming languages Perl
Computer skills Basic
Stability Stable
Source code URL https://codeload.github.com/berkeleyphylogenomics/flowerpower/zip/master
Maintained No

Maintainer


This tool is not maintained anymore.

Information


Unique identifier OMICS_13087
Name FlowerPower
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A seed sequence, a specified database from which putative homologs will be selected, and user-selected alignment quality control criteria (coverage and percent identity cutoffs)
Output data subfamily-HMM based alignment and a realignment of the sequences, functional subfamily, subfamily HMMs
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Source code URL https://codeload.github.com/berkeleyphylogenomics/flowerpower/zip/master
Maintained No

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Publication for FlowerPower

FlowerPower citations

 (9)
library_books

The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches

2015
GigaScience
PMCID: 4570625
PMID: 26380077
DOI: 10.1186/s13742-015-0083-4

[…] ods include GOFigure [], OntoBlast [], Gotcha [], GOPET [], the protein function prediction (PFP) method [, ], ConFunc [], and the extended similarity group (ESG) method []. Three methods, SIFTER [], FlowerPower [], and Orthostrapper [], use phylogenetic trees to transfer functions to target genes in the evolutionary context. There are other function prediction methods that consider coexpression p […]

library_books

In depth performance evaluation of PFP and ESG sequence based function prediction methods in CAFA 2011 experiment

2013
BMC Bioinformatics
PMCID: 3584938
PMID: 23514353
DOI: 10.1186/1471-2105-14-S3-S2

[…] tion information thoroughly from sequence database search results. These methods include PFP [,], ESG [], GOtcha [], GOPET [], OntoBlast [], GOFigure [], and ConFunc []. On the other hand, SIFTER [], FlowerPower [], and Orthostrapper [] employ phylogenetic trees to transfer functions to target genes in the evolutionary context. There are other function prediction methods considering co-expression […]

library_books

Evaluation of function predictions by PFP, ESG, and PSI BLAST for moonlighting proteins

2012
BMC Proc
PMCID: 3504920
PMID: 23173871
DOI: 10.1186/1753-6561-6-S7-S5

[…] arches [-]. Some recent Automatic Function Prediction (AFP) methods such as PFP [,], ESG [], Gotcha [], GOFigure [], and ConFunc [] use the Gene Ontology (GO) hierarchy. On the other hand, SIFTER [], FlowerPower [] and Orthostrapper [] employ phylogenetic trees to transfer functions to target genes in the evolutionary context. There are other function prediction methods that consider co-expression […]

library_books

Ortholog identification in the presence of domain architecture rearrangement

2011
Brief Bioinform
PMCID: 3178056
PMID: 21712343
DOI: 10.1093/bib/bbr036

[…] s problem uses a simple coverage criterion, e.g. requiring proteins to align over 70% of their lengths; this rule of thumb is reasonable for moderately sized proteins but may fail on longer proteins. FlowerPower [] uses subfamily hidden Markov models [] to iteratively retrieve and align homologous proteins followed by alignment analysis to provide high precision in selecting homologs with the same […]

library_books

Arabidopsis thaliana PGR7 Encodes a Conserved Chloroplast Protein That Is Necessary for Efficient Photosynthetic Electron Transport

2010
PLoS One
PMCID: 2908147
PMID: 20657737
DOI: 10.1371/journal.pone.0011688

[…] r to construct phylogenetic trees for selected regions of PGR7. PhyloBuilder provides a pipeline for automated phylogenomic analysis and domain prediction, starting with gathering homologs using the FlowerPower software . FlowerPower is similar to PSI-BLAST except that a set of subfamily hidden Markov models (HMMs) is used during the iterated search instead of a single profile during the iterated […]

library_books

Structural insights into the function of aminoglycoside resistance A1408 16S rRNA methyltransferases from antibiotic producing and human pathogenic bacteria

2010
Nucleic Acids Res
PMCID: 2995053
PMID: 20639535
DOI: 10.1093/nar/gkq627

[…] The KamB and NpmA protein sequences were used as search subjects in FlowerPower (), a clustering algorithm that can identify homologous sequences with similar domain architectures. The sequences retrieved were used in a BLAST search and a phylogenetic relatedness infe […]


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FlowerPower institution(s)
Department of BioEngineering, University of California, Berkeley, CA, USA; UC Berkeley and UCSF Joint Graduate Group in Bioengineering, University of California, CA, USA
FlowerPower funding source(s)
Presidential Early Career Award for Scientists and Engineers (PECASE) Grant #0238311 from the National Science Foundation, Grant #R01 HG002769-01 from the National Institutes of Health

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