PDEXK

Detects PD-(D/E)XK families. PDEXK is based on the binary classification of profile–profile alignments using support vector machines (SVMs). It is able to make confident assignments even for alignments that have statistically insignificant scores. The tool can be useful for other ‘problematic’ protein superfamilies, in which evolutionary relationships are not easily detectable by standard homology search methods.

PDEXK specifications

Web

Information

Unique identifier	OMICS_16767
Name	PDEXK
Interface	Web user interface
Restrictions to use	None
Input data	A paste protein sequence or multiple alignment.
Input format	FASTA
Output data	A sequence or multiple sequence alignment.
Computer skills	Basic
Stability	Stable
Maintained	Yes

Documentation

Documentation: http://bioinformatics.ibt.lt/pdexk/assets/ctx/0.0.1-SNAPSHOT/static_pages/help.html

Maintainer

Ceslovas Venclovas

Publication for PDEXK

Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile–profile alignments

2011 Nucleic Acids Res

PMCID: 3045609

PMID: 20961958

DOI: 10.1093/nar/gkq958

PDEXK institution(s)

Institute of Biotechnology, Vilnius, Lithuania

PDEXK funding source(s)

Supported by Howard Hughes Medical Institute and Ministry of Education and Science of Lithuania.

PDEXK reviews

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