FlowerPower statistics

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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

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Maintainer


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Publication for FlowerPower

FlowerPower in publications

 (7)
PMCID: 3584938
PMID: 23514353
DOI: 10.1186/1471-2105-14-S3-S2

[…] 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 […]

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

[…] [-]. 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 […]

PMCID: 3178056
PMID: 21712343
DOI: 10.1093/bib/bbr036

[…] 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 […]

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

[…] 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 […]

PMCID: 2995053
PMID: 20639535
DOI: 10.1093/nar/gkq627

[…] between the two extended structural motifs that define the functional specificity of the a1408 rrna methyltransferases., 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 […]


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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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