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FFPred specifications

Information


Unique identifier OMICS_22843
Name FFPred
Alternative names FFPred 2.0, FFPred 3
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Maintained Yes

Maintainer


  • person_outline Pr. David T. Jones

Publications for FFPred

FFPred citations

 (11)
library_books

De Novo characterization of transcriptomes from two North American Papaipema stem borers (Lepidoptera: Noctuidae)

2018
PLoS One
PMCID: 5783364
PMID: 29364900
DOI: 10.1371/journal.pone.0191061

[…] nnotations were filtered to retain only those corresponding to annotated arthropod genes (taxa: 6656, Arthropoda). Sequences lacking GO terms at this stage were subjected to additional analysis using FFPred 2.0, a “homology-independent” tool for GO term prediction []. The reliability of FFPred predictions is measured by the Matthews Correlation Coefficient (MCC) in the underlying support vector re […]

call_split

Overexpression of BdMATE Gene Improves Aluminum Tolerance in Setaria viridis

2017
Front Plant Sci
PMCID: 5462932
PMID: 28642761
DOI: 10.3389/fpls.2017.00865
call_split See protocol

[…] nces was generated using the Clustal Omega (). Analysis of conserved protein domains and the prediction of the molecular and cellular functions of these domains were evaluated by the online softwares FFPred and MEMSAT (; ). The phylogenetic tree was generated based on amino acid sequences of major grasses () that have been studied with MATE gene, using the Geneious software () for alignments and M […]

library_books

Genomic, Transcriptomic, and Proteomic Analysis Provide Insights Into the Cold Adaptation Mechanism of the Obligate Psychrophilic Fungus Mrakia psychrophila

2016
PMCID: 5100859
PMID: 27633791
DOI: 10.1534/g3.116.033308

[…] final gene set was mapped to KEGG pathways using KAAS (). GO annotations were retrieved from the results of InterProScan and Blast2GO (). Homology-independent GO annotations were also predicted using FFPred (). Transfer RNAs (tRNAs) were predicted using tRNAScan-SE (). Other genome sequences and annotations used in comparative genomic analysis were downloaded from JGI (http://genome.jgi.doe.gov). […]

library_books

Evolution of the Twist Subfamily Vertebrate Proteins: Discovery of a Signature Motif and Origin of the Twist1 Glycine Rich Motifs in the Amino Terminus Disordered Domain

2016
PLoS One
PMCID: 4996418
PMID: 27556926
DOI: 10.1371/journal.pone.0161029

[…] The programs in the FFpred-server were used to assess for any disordered domains and for function prediction []. The Phyre2 Structure Prediction server [] was used to construct a representation of the secondary structure […]

library_books

SVM Prot 2016: A Web Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity

2016
PLoS One
PMCID: 4985167
PMID: 27525735
DOI: 10.1371/journal.pone.0155290

[…] These proteins were not in the SVM-Prot training datasets but with available sequence in the literature or public databases. summarized the prediction results of those 42 novel proteins by SVM-Prot, FFPred 3 [] and NCBI BLAST [], and the detailed prediction results were further provided in . The function of a novel protein was considered as matched to a computer identified functional family when […]

library_books

New genetic regulators question relevance of abundant yolk protein production in C. elegans

2015
Sci Rep
PMCID: 4639837
PMID: 26553710
DOI: 10.1038/srep16381

[…] howing that its protein-coding sequence underlies the observed phenotype. Absence of similarities in BLAST searches support its Caenorhabditis-specific character. The homology-independent search tool FFPred 2.0 predicts VRP-1 to be involved in DNA-dependent regulation of transcription, further supported by its nuclear localization (see below).Premature stop and splice site variants were similarly […]


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FFPred institution(s)
Bioinformatics Group, Department of Computer Science, University College London, London, UK
FFPred funding source(s)
Supported by the UK Biotechnology and Biological Sciences Research Council (References: BB/L020505/1 and BB/L002817/1).

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