TMB Finding Pipeline:  Novel Approach for Detecting β-Barrel Membrane Proteins in Genomic Sequences

2007 ◽  
Vol 47 (6) ◽  
pp. 2456-2461 ◽  
Author(s):  
M. Michael Gromiha ◽  
Yukimitsu Yabuki ◽  
Makiko Suwa
Keyword(s):  
Membrane Proteins ◽  
Genomic Sequences ◽  
Novel Approach

scholarly journals All fingers are not the same: Handling variable-length sequences in a discriminative setting using conformal multi-instance kernels

2017 ◽  
Author(s):  
Sarvesh Nikumbh ◽  
Peter Ebert ◽  
Nico Pfeifer
Keyword(s):  
Binary Classification ◽  
Positional Information ◽  
Weight Vector ◽  
Variable Length ◽  
Genomic Sequences ◽  
String Kernels ◽  
Promoter Sequences ◽  
Novel Approach ◽  
The Individual ◽  
Visualization Techniques

AbstractMost string kernels for comparison of genomic sequences are generally tied to using (absolute) positional information of the features in the individual sequences. This poses limitations when comparing variable-length sequences using such string kernels. For example, profiling chromatin interactions by 3C-based experiments results in variable-length genomic sequences (restriction fragments). Here, exact position-wise occurrence of signals in sequences may not be as important as in the scenario of analysis of the promoter sequences, that typically have a transcription start site as reference. Existing position-aware string kernels have been shown to be useful for the latter scenario.In this work, we propose a novel approach for sequence comparison that enables larger positional freedom than most of the existing approaches, can identify a possibly dispersed set of features in comparing variable-length sequences, and can handle both the aforementioned scenarios. Our approach, CoMIK, identifies not just the features useful towards classification but also their locations in the variable-length sequences, as evidenced by the results of three binary classification experiments, aided by recently introduced visualization techniques. Furthermore, we show that we are able to efficiently retrieve and interpret the weight vector for the complex setting of multiple multi-instance kernels.

scholarly journals A novel approach to analyze membrane proteins by laser mass spectrometry: From protein subunits to the integral complex

2007 ◽  
Vol 18 (8) ◽  
pp. 1429-1438 ◽  
Author(s):  
Nina Morgner ◽  
Thomas Kleinschroth ◽  
Hans-Dieter Barth ◽  
Bernd Ludwig ◽  
Bernhard Brutschy
Keyword(s):  
Mass Spectrometry ◽  
Membrane Proteins ◽  
Laser Mass Spectrometry ◽  
Protein Subunits ◽  
Novel Approach

scholarly journals Biochemical analysis of ligand-induced receptor patching and capping using a novel immunolactoperoxidase iodination technique.

1979 ◽  
Vol 83 (3) ◽  
pp. 649-656 ◽  
Author(s):  
L Y Bourguignon
Keyword(s):  
Membrane Proteins ◽  
Biochemical Analysis ◽  
Polyacrylamide Gel Electrophoresis ◽  
Histocompatibility Antigen ◽  
Surface Proteins ◽  
Cell Surface Proteins ◽  
Cytochemical Analysis ◽  
Novel Approach ◽  
Surface Receptor ◽  
Specific Ligand

A novel approach for the analysis of membrane proteins involved in ligand-induced surface receptor patching and capping is described. The technique is based on the use of immunolactoperoxidase (immuno-LPO) conjugates which catalyze the iodination of those surface proteins with available tyrosine groups that are located in the immediate vicinity of the patch or cap of a particular antigen. We have used the patching and capping of the H-2 (histocompatibility) antigen on mouse thymocytes to illustrate this method. However, this technique should be generally applicable to any cell surface proteins which can be induced to form patches or caps by a specific ligand. Cytochemical analysis indicates that the immuno-LPO conjugates induce the same patching and capping of the H-2 antigen as does the unconjugated antibody. Biochemical analysis of the 125I-labeled proteins by SDS polyacrylamide gel electrophoresis indicates that a large membrane protein (mol wt of approximately 200,000 daltons) is closely associated with H-2 patches and caps. Since a number of other prominent membrane proteins are not labeled by this procedure, selective redistribution of certain surface proteins must be occurring during H-2 antibody-induced patching and capping.

scholarly journals TMBETA-GENOME: database for annotated  -barrel membrane proteins in genomic sequences

2007 ◽  
Vol 35 (Database) ◽  
pp. D314-D316 ◽  
Author(s):  
M. M. Gromiha ◽  
Y. Yabuki ◽  
S. Kundu ◽  
S. Suharnan ◽  
M. Suwa
Keyword(s):  
Membrane Proteins ◽  
Genomic Sequences ◽  
Genome Database

scholarly journals Author Correction: De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Nikolaos Vakirlis ◽  
Omer Acar ◽  
Brian Hsu ◽  
Nelson Castilho Coelho ◽  
S. Branden Van Oss ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
De Novo ◽  
Genomic Sequences

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20609-y.

Sign in / Sign up

Export Citation Format

Share Document