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FunFHMMer specifications


Unique identifier OMICS_08428
Name FunFHMMer
Interface Web user interface
Restrictions to use None
Input data Protein sequence in FASTA format or UniProt/GenBank sequence identifiers
Output data The output of the web server provides the multidomain architecture of the query sequence along with CATH domain superfamily and FunFam assignments for each domain identified within the query sequence.
Computer skills Basic
Stability Stable
Maintained Yes




  • person_outline Sayoni Das

Publications for FunFHMMer

FunFHMMer citations


Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

PLoS One
PMCID: 5927432
PMID: 29709017
DOI: 10.1371/journal.pone.0193922

[…] s the hierarchical classification of protein domains on the basis of their associated folding patterns for the entered query. The functional characterization of the query sequences was analyzed using FunFHMMer web server [] to evaluate their functional annotations based on gene ontological terms. Further, the ReviGO analysis, based on a hypergeometric dis […]


HMMER Cut off Threshold Tool (HMMERCTTER): Supervised classification of superfamily protein sequences with a reliable cut off threshold

PLoS One
PMCID: 5868777
PMID: 29579071
DOI: 10.1371/journal.pone.0193757

[…] r function shifts by means of the identification of Specificity Determining Positions (SDPs), resulting in the FunShift database []. GEMMA was used to subcluster the CATH-Gene3D resource resulting in FunFHMMER []. Here an automated cut-off was provided by a functional coherence index, also based on SDPs. CDD [] is a domain database that includes an automated hierarchical classification of subfamil […]


Gene3D: Extensive prediction of globular domains in proteins

Nucleic Acids Res
PMCID: 5753370
PMID: 29112716
DOI: 10.1093/nar/gkx1069

[…] As in the previous release we added CATH-FunFam annotations produced by the FunFHMMer pipeline (). In this release we also provide Pfam-FunFam annotations. These annotations were shown to be valuable for functional prediction (). We have expanded our structural annotations to […]


An overview of comparative modelling and resources dedicated to large scale modelling of genome sequences

Acta Crystallogr D Struct Biol
PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] odels were found to be of similar quality to those built using close sequence homologues (≥30% sequence identity) as parents (Lee et al., 2010).A recent, more accurate FunFam identification protocol (FunFHMMer; Das et al., 2015) uses similarities in sequence patterns, reflecting highly conserved positions and specificity-determining positions, to guide subclustering and family detection. Highly co […]


Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach

Front Plant Sci
PMCID: 5447077
PMID: 28611792
DOI: 10.3389/fpls.2017.00819

[…] fication of the identified protein sequences was done using CATH server (Sillitoe et al., ). The functional classification of the identified CATH superfamilies were done using FunFHMMer (Das et al., ) which scans the input protein sequences against CATH FunFam HMMs and the functional annotation were further analyzed based on gene o […]


An Atlas of Peroxiredoxins Created Using an Active Site Profile Based Approach to Functionally Relevant Clustering of Proteins

PLoS Comput Biol
PMCID: 5302317
PMID: 28187133
DOI: 10.1371/journal.pcbi.1005284

[…] ltiple isofunctional families. Our goal is to develop a method to more automatically identify isofunctional clusters.Several approaches aim to cluster sequences into isofunctional clusters, including FunFHMMer [] (an updated version of GeMMA []), SCI-PHY [], and ASMC []. These methods start with known superfamily sequences and subdivide that large set using clustering and pattern recognition of fu […]

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FunFHMMer institution(s)
Institute of Structural and Molecular Biology, UCL, Darwin Building, Gower Street, UK
FunFHMMer funding source(s)
UCL Overseas Research Scholarship; Biotechnology and Biological Sciences Research Council (BBSRC) [BB/K020013/1]; the Wellcome Trust [081989/Z/07/Z]; EU

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