GiG.DB: Quadruplex database of G4-iM Grinder.
In EfresBR/G4iMGrinder: G4iMGrinder: G4 Quadruplex, i-Motif and higher-order structures in DNA and RNA sequences search and analysis tool.

GiG.DB.rda

R Documentation

Quadruplex database of G4-iM Grinder.

Database of DNA and RNA, G4s and i-Motifs, forming and non-forming structures and their characteristics. Database is divided in four data frames.

1. GiG.DB.BioInformatics, contains the sequences to be found by G4-iM Grinder and information.

2. GiG.DB.Refs, contains the sequences' bibliographical documentation.

3. GiG.DB.BioPhysical, contains the sequences' biophysical-related information.

4. Version, contains the version information of the database.

data(GiG.DB$GiG.DB.BioInformatics)
data(GiG.DB$GiG.DB.Refs)
data(GiG.DB$GiG.DB.BioPhysical)
data(GiG.DB$Version)

...

Quadruplex: logical, does the sequence form a quadruplex. TRUE for yes, FALSE for no.
Genome: factor, genome type (DNA or RNA)
Nucleotide: factor, run-nucleotide composition (G or C)
Name: character, the name of the quadruplex/sequence. Must be unique in Bioinformatics dataframe. Must have entry in Refs data frame.
Sequence: character, the nucleotide arrangement of the sequence. Must be unique in Bioinformatics dataframe.
Length: integer, the length in nucleotides of the quadruplex sequence
Tm: integer, Number of biophysical entries within the GiG.DB$GiG.DB.BioPhysical dataframe in relationship with the sequence.

Name: character, the name of the quadruplex/sequence. Used as ID to link with Bioinformatics data frame. Must be unique in Refs data frame. Must have an equal entry in Bioinformatics dataframe.
DOI: character, DOI code of article where sequence was published.
Pubmed: character, PubMedID code of article where sequence was published.
comments: character, Other information and comments of article where sequence was published.

Name: character, the name of the quadruplex/sequence. Used as ID to link with Bioinformatics data frame. Must have an equal entry in Bioinformatics and Refs dataframe.
Tm: integer, experimental melting temperature (Tm) of the entry in degrees.
pH: integer, experimental pH of the entry.
CC.Sequence.uM: integer, experimental micromolar concentration of the DNA or RNA sequence in solution of the entry.
CC.K.mM: integer, experimental milimolar concentration of potassium ions in solution of the entry.
CC.Na.mM: integer, experimental milimolar concentration of sodium ions in solution of the entry.
Topology: factor, found experimental topology of the entry.