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GC-Profile specifications

Information


Unique identifier OMICS_23361
Name GC-Profile
Software type Application/Script
Interface Web user interface
Restrictions to use None
Input format FASTA
Output data A graph.
Programming languages Perl
Computer skills Basic
Maintained No

Maintainer


This tool is not available anymore.

Publication for GC-Profile

GC-Profile in pipelines

 (3)
2017
PMCID: 5357945
PMID: 28317865
DOI: 10.1038/srep44786

[…] of the distribution of core genes and unique genes, two large genomic islands have been detected (gi-i: from 3812417 to 4085811 bp and gi-ii: from 4171990 to 4395111 bp) in s. lydicus 103 based on gc-profile ( and ). it is thought that streptomyces achieves the productivity of a wide variety of secondary metabolites by acquiring foreign biosynthetic enzyme genes through horizontal gene […]

2017
PMCID: 5430456
PMID: 28424524
DOI: 10.1038/s41598-017-01176-7

[…] were predicted by using the rast and genemark applications, . after gene prediction, nucleotide and aminoacid sequence analyses were made using blast. g + c content was calculated using the web tool gc-profile. for each protein encoded by the fosmid f1017.1h, homologous protein sequences were retrieved from ncbi after identification by blast x. multiple sequence alignments and phylogenetic trees […]

2015
PMCID: 4527741
PMID: 26248285
DOI: 10.1371/journal.pone.0135104

[…] []. cvtree, a whole genome-based, alignment-free composition vector (cv) method was performed for the phylogenetic analysis [], and a phylogenetic tree was generated using the mega program []. the gc-profile was used to compute the gc content variation in dna sequences and predict the genomic islands []. the circular chromosome map was created using the program cgview []. the sequence […]


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GC-Profile in publications

 (100)
PMCID: 5922379
PMID: 29721185
DOI: 10.18632/oncotarget.24901

[…] the tumor expression profile, dnmt3a overexpression was significantly correlated with bcl2 protein expression (p = 0.0261). conversely, dnmt3a expression status was not correlated with the gc or non-gc profile, or with p53, myc and ki67 expression (table ). no significant correlation between dot1l expression and the phenotypic parameters was identified (table )., dnmt3a protein overexpression […]

PMCID: 5915959
PMID: 29713692
DOI: 10.1210/js.2018-00021

[…] and other peripheral oscillators, including the adrenal clock, presumably by the action of food-entrainable oscillators in the dorsomedial hypothalamus [, , ]. under this condition, the daily gc profile has two distinct peaks per day, strongly suggesting that the circadian gc rhythm is produced by the integrated activity of feeding-independent scn central clock and food-entrainable local […]

PMCID: 5871888
PMID: 29593241
DOI: 10.1038/s41598-018-23708-5

[…] using einverted (http://emboss.bioinformatics.nl/cgi-bin/emboss/einverted). the search for palindromic dna was made using the meme web-tool. gc content profile and gc-skew were obtained using gc-profile and genskew (http://genskew.csb.univie.ac.at/), respectively., the pchv1 complete sequence is available at genbank (accession number - mg651603). fastq file is also available […]

PMCID: 5850279
PMID: 29563925
DOI: 10.3389/fgene.2018.00066

[…] the human (this table). the gc contents of whole sequences and of large esl are, respectively, about 10 and 14 percentage units below averages of other mammals. the gc differences point to a lower-gc profile, somewhat similar to that in insect-2 group. some data rows or columns are rendered in italics to improve the readability., as seen in table , esl15 and esl27 are quite longer (at […]

PMCID: 5852592
PMID: 29443947
DOI: 10.3390/genes9020096

[…] for at (dapi) and for gc (chromomycin a3 (cma3), 7-amino-actinomycin d (7-aad), propidium iodide). this is a particularly useful approach in combination with bioinformatics analysis producing at/gc profile across chromosomes/lgs hence quantifying cytogenetic data. basically, there are two possible approaches producing at/gc profiles across linkage group/chromosome: (1) chromoplot [] […]


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GC-Profile institution(s)
Department of Physics, Tianjin University, Tianjin, China
GC-Profile funding source(s)
Supported by NNSF of China Grant No. 90408028.

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