What is Rampage?
RNA annotation and mapping of promoters for analysis of gene expression (RAMPAGE) is a method that harnesses highly specific sequencing of 5'-complete complementary DNAs to identify transcription start sites (TSSs) genome-wide. Although TSS mapping has historically relied on detection of 5'-complete cDNAs, current genome-wide approaches typically have limited …
What is Ramage annotation and mapping?
11/11/2013 · RAMPAGE allows for highly stringent selection of 5′-complete molecules, thus allowing base-resolution TSS identification with a high signal-to-noise ratio. Paired-end sequencing of medium-length cDNAs yields transcript structure information that is essential to interpreting the relationship of TSSs to annotated genes and transcripts. As opposed to …
What is the difference between ProCheck and Rampage?
RAMPAGE which will accept any PDB file you provide. Using PDB 1HMP as an example, this is the sort of figure MOLEMAN2 produces (cropped for display): MolProbity produces very nice images like this, extracted from this output : This even more beautiful figure is from RAMPAGE, and shows the four plots combined. It was extracted from this output which also contains the data …
How many plots are there in Rampage?
Rampage Server 3. SFCHECK 4. The NQ-Flipper page (1) PROCHECK: It checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.
What is rampage in bioinformatics?
DESCRIPTION. RAMPAGE is an offshoot of RAPPER which generates a Ramachandran plot using data derived by the Richardsons and coworkers. ... The Ramachandran diagram plots phi versus psi dihedral angles for each residue in the input pdb file.
What is verify3d?
Determines the compatibility of an atomic model (3D) with its own amino acid sequence (1D) by assigning a structural class based on its location and environment (alpha, beta, loop, polar, nonpolar etc) and comparing the results to good structures.
What is Q mean score?
QMEAN, which stands for Qualitative Model Energy ANalysis, is a composite scoring function describing the major geometrical aspects of protein structures. Five different structural descriptors are used. The local geometry is analyzed by a new kind of torsion angle potential over three consecutive amino acids.
What does a Ramachandran plot show?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963).
How do you read 3D results?
On verify3D, a score of more than 80% means that your model has good quality - however you must check with other evaluation tolls such as voromqa, Proq3 etc to make sure you have a high quality model.
How do you cite Pdbsum?
PDBsum is a database that provides an overview of the contents of each 3D macromolecular structure deposited in the Protein Data Bank....PDBsum.ContentAuthorsRoman Laskowski & al. (1997)Primary citationPMID 9433130AccessWebsitewww.ebi.ac.uk/pdbsum/8 more rows
What is Z score in SWISS-MODEL?
In SWISS-MODEL the QMEAN z-score represents an estimate of how comparable the model is to experimentally derived structures of similar size. QMEAN z-scores around zero indicate good agreement between the model structure and experimental structures of similar size.
What does GMQE mean?
GMQE (Global Model Quality Estimation) is is expressed as a number between 0 and 1, reflecting the expected accuracy of a model built with that alignment and template, normalized by the coverage of the target sequence. Higher numbers indicate higher reliability.
What is GMQE?
GMQE (Global Model Quality Estimate) is a quality estimate which combines properties from the target-template alignment and the template structure.
What angle is phi?
-140 degreesTypical values are phi = -140 degrees and psi = 130 degrees. In contrast, alpha-helical residues have both phi and psi negative.
What is the difference between torsion angle and dihedral angle?
The angle between two bonds A torsion angle, also known as a dihedral angle, is formed by three consecutive bonds in a molecule and defined by the angle created between the two outer bonds. The backbone of a protein has three different torsion angles.01-Feb-2020
What is disallowed region in Ramachandran plot?
Disallowed regions generally involve steric hindrance between the side chain C-beta methylene group and main chain atoms. Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot.