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.

Description

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.

Usage

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

Format

...

1. GiG.DB$GiG.DB.BioInformatics

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.

2. GiG.DB$GiG.DB.Refs

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.

3. GiG.DB$GiG.DB.BioPhysical

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.

4. GiG.DB$Version

Name

factor, data frames within GiG.DB.

Tm

integer, version of data frames.

Examples

data(GiG.DB)
View(GiG.DB)

EfresBR/G4iMGrinder documentation built on June 11, 2021, 2:57 a.m.