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 in publications

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

[…] 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 […]

PMCID: 5571743
PMID: 28777078
DOI: 10.1107/S2059798317008920

[…] 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 […]

PMCID: 5447077
PMID: 28611792
DOI: 10.3389/fpls.2017.00819

[…] 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 […]

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

[…] 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 […]

PMCID: 4917113
PMID: 27332861
DOI: 10.1371/journal.pcbi.1004926

[…] beta-lactamases, the most highly populated and clinically relevant class, to identify fds implicated in the distinct phenotypes associated with different class a types and variants. we show that our funfhmmer method can separate the known beta-lactamase classes and identify those positions likely to be responsible for the different implementations of the mechanism of action in these enzymes. two […]

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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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