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pepStat specifications

Information


Unique identifier OMICS_04027
Name pepStat
Software type Package/Module
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 pepStat

pepStat citations

 (8)
library_books

In silico functional elucidation of uncharacterized proteins of Chlamydia abortus strain LLG

2017
PMCID: 5351547
PMID: 28344832
DOI: 10.4155/fsoa-2016-0066

[…] additionally, the properties of sequences including aromatic and aliphatic, basic and acidic sequences with average number of polar and nonpolar amino acids were determined by using emboos pepstat []. to discover the position of these proteins with predicted signature sequences, tmhmm [], hmmtop [] and sosui-gramn [] were used, while subcellular localization of proteins was determined […]

library_books

Catalysis and Structure of Zebrafish Urate Oxidase Provide Insights into the Origin of Hyperuricemia in Hominoids

2016
PMCID: 5138847
PMID: 27922051
DOI: 10.1038/srep38302

[…] atomic coordinates of druox. the number of cysteines in uox proteins of different taxonomic divisions was determined for 1385 sequences clustered at 80% similarity with the cdhit program using the pepstat program of the emboss package. data were plotted using the geom_boxplot and geom_jitter functions of the ggplot2 library of the r package., catalytic activity measurements were carried […]

library_books

In Silico Phylogenetic Analysis and Molecular Modelling Study of 2 Haloalkanoic Acid Dehalogenase Enzymes from Bacterial and Fungal Origin

2016
PMCID: 4736600
PMID: 26880911
DOI: 10.1155/2016/8701201

[…] acid dehalogenase from bacterial and fungal sources were retrieved from the ncbi database (http://www.ncbi.nlm.nih.gov/protein/). the amino acid composition of these sequences was computed using pepstat module integrated in the emboss software []. multiple sequence alignment for individual profiles was performed using muscle and phylogenetic analysis using mega 6 software []. the discovered […]

library_books

Protein Thermostability Is Owing to Their Preferences to Non Polar Smaller Volume Amino Acids, Variations in Residual Physico Chemical Properties and More Salt Bridges

2015
PMCID: 4503463
PMID: 26177372
DOI: 10.1371/journal.pone.0131495

[…] two hundred mesophilic proteins (table a in ) were downloaded and the percentage of 20 amino acids in each protein was calculated by accessing the website http://www.ebi.ac.uk/tools/services/pepstat []. the frequency zone was arranged in ascending order. here, the sturges formula (k = 1+3.322 log10 n) was used to find the class interval and desirable number of groups […]

library_books

In silico characterization of putative drug targets in Staphylococcus saprophyticus, causing bovine mastitis

2013
PMCID: 3669785
PMID: 23750077
DOI: 10.6026/97320630009339

[…] is required to find out the surface membrane proteins which could be probable drug targets. further these surface membrane pathway protein sequences were characterized by using peptide statistic (pepstat) program which is available online via european molecular biology open software suite (emboss) web server []., the bacteria used in the present study could be identified as s. saprophyticus […]

library_books

A top down approach to classify enzyme functional classes and sub classes using random forest

2012
PMCID: 3351021
PMID: 22376768
DOI: 10.1186/1687-4153-2012-1

[…] having the largest bank of sequences. the number of sequences shown represent sequences with 100% reduced identity., to extract sequence-derived features, we used two online tools, emboss-pepstat: an online tool that generates a list of 61 feature values for a given sequence [], and protparams: an online tool that computes values for 36 sequence features []. pepstats generates values […]


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pepStat institution(s)
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA

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