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This is a list of tools and resources that we have found mentioned in this publication.


WEBLOGO (tool)

RRID:SCR_010236

A web based application designed to make the generation of sequence logos as easy and painless as possible. Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.

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Promega (tool)

RRID:SCR_006724

An Antibody supplier

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UCSF Chimera (tool)

RRID:SCR_004097

A highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use.

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LIMMA (tool)

RRID:SCR_010943

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

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GE Healthcare (tool)

RRID:SCR_000004

A commercial antibody supplier and provider of various services.

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Monoclonal ANTI-FLAGĀ® M2 antibody (antibody)

RRID:AB_262044

This monoclonal antibody targets FLAG

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Ub (P4D1) antibody (antibody)

RRID:AB_628423

This monoclonal antibody targets Ub (P4D1)

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Adobe Photoshop (tool)

RRID:SCR_014199

Software for image processing, analysis, and editing. The software includes features such as touch capabilities, a customizable toolbar, 2D and 3D image merging, and Cloud access and options.

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Clustal Omega (tool)

RRID:SCR_001591

Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

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MODELLER: Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints (tool)

RRID:SCR_008395

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download for most Unix/Linux systems, Windows, and Mac. Several graphical interfaces to MODELLER are commercially available. There are also many other resources and people using Modeller in graphical or web interfaces or other frameworks. Sponsors: This resource is suppored by the Sandler Family Supporting Foundation, NIH R01 GM54762, P01 GM71790, P01 A135707, and U54 GM62529, as well as hardware gifts from IBM and Intel. Keywords: Homology, Comparative, Model, Protein, 3-Dimentional, Structure, Alignment, Sequence, Hydrogen, Atom, Sequence, Database, Cluster, Comparison,

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MUSCLE (tool)

RRID:SCR_011812

Data analysis service for MUltiple Sequence Comparison by Log- Expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options.

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Chimera (tool)

RRID:SCR_002959

A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools.

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Microsoft Excel (tool)

RRID:SCR_016137

Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.

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Adobe Illustrator (tool)

RRID:SCR_010279

Vector graphics software to create digital graphics, illustrations, and typography for several types of media: print, web, interactive, video, and mobile.

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ImageQuant (tool)

RRID:SCR_014246

Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images.

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