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AFP-Pred specifications

Information


Unique identifier OMICS_25181
Name AFP-Pred
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for AFP-Pred

AFP-Pred citations

 (4)
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An Effective Antifreeze Protein Predictor with Ensemble Classifiers and Comprehensive Sequence Descriptors

2015
Int J Mol Sci
PMCID: 4613249
PMID: 26370959
DOI: 10.3390/ijms160921191
call_split See protocol

[…] the current method objectively, comparisons are carried out for AFP-Ensemble and previously-published methods on the independent testing dataset. reports the detailed prediction results obtained by AFP-Pred [], AFP-PSSM [], AFP-PseAAC [] and AFP-Ensemble. AFP-Pred combines the predicted secondary structure information and physicochemical properties. AFP-PSSM is mainly based on the information ex […]

library_books

Microbial Consortium Associated with the Antarctic Marine Ciliate Euplotes focardii: An Investigation from Genomic Sequences

2015
Microb Ecol
PMCID: 4494151
PMID: 25704316
DOI: 10.1007/s00248-015-0568-9

[…] Rhodobacteraceae bacterium HTCC2083 [] and one sequence sharing 45 % similarity to type II AFP from the catadromous fish Lates calcarifer []. Finally, we performed a prediction of putative AFP using AFP-Pred and iAFP bioinformatic tool as described above. Following this approach, we found 2755 or 600 (using AFP-Pred respectively iAFP) contigs that potentially encode AFPs in Gammaproteobacteria, 2 […]

library_books

Bacterial Ice Crystal Controlling Proteins

2014
PMCID: 3918373
PMID: 24579057
DOI: 10.1155/2014/976895

[…] [].With these similarities in mind, Doxey et al. [] were able to develop a antifreeze prediction program, AFPredictor. Another prediction program by Kandaswamy and colleagues [], the machine learning AFP-pred, shows some promise of detecting important antifreeze peptide features. However, using a training set of sequences consisting of hypothetical and unconfirmed antifreeze proteins indicates tha […]

library_books

Genome wide gene expression analysis of facultative reproductive diapause in the two spotted spider mite Tetranychus urticae

2013
BMC Genomics
PMCID: 4046741
PMID: 24261877
DOI: 10.1186/1471-2164-14-815

[…] n database of NCBI also hit to antifreeze proteins of Coleoptera with a low to moderate E-value (between 1e-02 and 1e-06). Furthermore, all members from this family were predicted as an insect AFP by AFP-Pred, a recently developed software tool using a “random forest” approach for the prediction of antifreeze proteins [].Accordingly, we aligned and compared the T. urticae mite sequences with well- […]

Citations

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AFP-Pred institution(s)
Institute for Neuro- and Bioinformatics, University of Lübeck, Lübeck, Germany; Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Lübeck, Germany; Gordon Life Science Institute, San Diego, CA, USA; School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, Singapore; Bharathidasan University, Tiruchirappalli, India; Laboratory of Structural Biochemistry, Genome Institute of Singapore, Singapore, Singapore
AFP-Pred funding source(s)
Supported by the Graduate School for Computing in Medicine and Life Sciences funded by Germany’s Excellence Initiative [DFG GSC 235/1].

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