SDPfox specifications

Information


Unique identifier OMICS_07159
Name SDPfox
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_07159
Name SDPfox
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Publication for SDPfox

SDPfox in publications

 (8)
PMCID: 4815063
PMID: 27030133
DOI: 10.1186/s12864-016-2590-9

[…] families mapt, map2 and map4 and within the mtbds. this issue was addressed by examining the region containing the 4 well-conserved mtbds in these subfamilies with programs such as sdpclust or sdpfox [] that measure both the level of amino acid conservation at each site and the significance of any conserved changes (i.e. aa replacements) characteristic of paralogous divergence. a composite […]

PMCID: 4746308
PMID: 26904004
DOI: 10.3389/fmicb.2016.00128

[…] of the analyzed genomes, the ncbi taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) was used. to predict substrate specificities according to the specificity-determining positions (sdp), the sdpfox web tool (mazin et al., ) was used with the maximum percent of gaps allowed in a group in each column being 50%. as an input for the sdp analysis, we used multiple alignments […]

PMCID: 4720485
PMID: 26788940
DOI: 10.1371/journal.pcbi.1004701

[…] can be determined by statistical methods. sdps are cdps that affect function and are identified by cross analyzing the obtained data with mutual information (mi). sdps. cdps were determined using sdpfox [] and mistic [] was used to determine mi. a table with the results of the performed sdp and mi analysis is available at ., the starting structures for modeling all studied trhbs corresponds […]

PMCID: 4079213
PMID: 24869856
DOI: 10.1093/gbe/evu110

[…] of transmembrane helices was made with tmhmm server () (http://www.cbs.dtu.dk/services/tmhmm/, last accessed june 13, 2014)., for the cdp analyses, three different software packages were used. sdpfox () (http://bioinf.fbb.msu.ru/sdpfoxweb/main.jsp, last accessed june 13, 2014) was used with default parameters, allowing a maximum of 30% of gaps in a group per column. groupsim () […]

PMCID: 3962155
PMID: 24688747
DOI: 10.5936/csbj.201308007

[…] abilities of several methods (real-valued et [], cumulative mutual information (mi) [], proximity mi [], evolutionary trace integer value [], and the methods designed for the identification of sdps (sdpfox and xdet) []) to identify catalytic residues in enzymes, in order to investigate the extents to which the predictive powers of the different methods overlap. the results revealed […]


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SDPfox institution(s)
Cellnetworks, University of Heidelberg, Heidelberg, Germany

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