Assemble2 2.3 – Construct & Study RNA Architectures

Assemble2 2.3

:: DESCRIPTION

Assemble proposes an intuitive graphical interface to study and construct complex three-dimensional RNA structures. When an RNA tertiary structure is opened with Assemble, it is automatically annotated with a secondary structure definition. This secondary structure can be used as a map to analyze the original tertiary structure. Using a secondary structure definition, Assemble can also produce a first draft of a 3D Model. Then the construction process can be pursued “by hand” using several widgets.

::DEVELOPER

Dr. Fabrice Jossinet at the laboratory of Pr. Eric Westhof

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Assemble

:: MORE INFORMATION

Citation

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
Fabrice Jossinet; Thomas E Ludwig; Eric Westhof
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq321

ORCA – Genomics Research Container Architecture

ORCA

:: DESCRIPTION

ORCA is a platform for bioinformatics analysis. It is suited for those wishing to conduct self-serve analysis using their own existing data. Hundreds of bioinformatics tools from Brewsci/bio are installed in the ORCA Docker image using Linuxbrew.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ORCA

:: MORE INFORMATION

Citation

Jackman SD, Mozgacheva T, Chen S, O’Huiginn B, Bailey L, Birol I, Jones SJM.
ORCA: a comprehensive bioinformatics container environment for education and research.
Bioinformatics. 2019 Nov 1;35(21):4448-4450. doi: 10.1093/bioinformatics/btz278. PMID: 31004474; PMCID: PMC6821186.

PDART – Protein Domain Architecture Retrieval Tool

PDART

:: DESCRIPTION

PDART is a web site to compare domain architectures or proteins.

:: DEVELOPER

Laboratory of Computational Molecular Biology, Beijing Normal University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Sep 1;22(17):2081-6. Epub 2006 Jul 12.
An initial strategy for comparing proteins at the domain architecture level.
Lin K1, Zhu L, Zhang DY.

DAMA – Protein Domain Architectures

DAMA

:: DESCRIPTION

DAMA (Domain Annotation by a Multi-objective Approach) is a novel approach that identifies architectures through a multi-objective optimisation algorithm combining scores of domain matches, previously observed multi-domain co-occurrence, and domain overlapping.

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 DAMA

:: MORE INFORMATION

Citation

A multi-objective optimisation approach accurately resolves protein domain architectures.
Bernardes JS, Vieira FR, Zaverucha G, Carbone A.
Bioinformatics. 2015 Oct 12. pii: btv582.

normGAM – Remove Systematic Biases in Genome Architecture Mapping data

normGAM

:: DESCRIPTION

normGAM is an R package for normalizing genome architecture mapping (GAM) data. It implements five normalization methods, including normalized linkage disequilibrium (NLD), vanilla coverage (VC), sequential component normalization (SCN), iterative correction and eigenvector decomposition (ICE), and Knight-Ruiz 2-norm (KR2). The normalization procedure can remove known and unknown systematic biases, the known biases including window detection frequency, fragment length, mappability, and GC content.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

normGAM

:: MORE INFORMATION

Citation

Liu T, Wang Z.
normGAM: an R package to remove systematic biases in genome architecture mapping data.
BMC Genomics. 2019 Dec 30;20(Suppl 12):1006. doi: 10.1186/s12864-019-6331-8. PMID: 31888469; PMCID: PMC6936146.

ArchiP 2.3 – Detecting Architectures of all-β and α/β-classes

ArchiP 2.3

:: DESCRIPTION

ArchiP detects architectures of all-β and α/β-classes

::DEVELOPER

Evgeniy Aksianov (evaksianov@gmail.com)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 ArchiP

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2012 Apr;10(2):1241003. doi: 10.1142/S021972001241003X.
SheeP: A tool for description of β-sheets in protein 3D structures.
Aksianov E, Alexeevski A.

XSTREAM – Variable Sequence Tandem Repeats Extraction and Architecture Modeling

XSTREAM

:: DESCRIPTION

XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify “fundamental” tandem repeat patterns.

::DEVELOPER

Newman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Oct 11;8:382.
XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences.
Newman AM, Cooper JB.

ProtOn 1603061903 – Description of Protein 3D structure in terms of Architecture, Topology and Motifs

ProtOn 1603061903

:: DESCRIPTION

ProtOn (Proteins Online): 1) draws β-sheet maps, 2) detects architectures of all-β and α/β-classes and 3) detects structural motifs containing β-strands

::DEVELOPER

Evgeniy Aksianov (evaksianov@gmail.com)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

  ProtOn

:: MORE INFORMATION

SMART 8.0 – Analysis of Protein Domain Architectures

SMART 8.0

:: DESCRIPTION

SMART (Simple Modular Architecture Research Tool) is an online resource for the identification and annotation of protein domains and the analysis of protein domain architectures.More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Letunic I, Doerks T, Bork P
SMART: recent updates, new developments and status in 2015
Nucleic Acids Res 2014; doi:10.1093/nar/gku949

Letunic et al. (2012)
SMART 7: recent updates to the protein domain annotation resource
Nucleic Acids Res , doi:10.1093/nar/gkr931

GiA Roots – Analysis of Plant Root system Architecture

GiA Roots

:: DESCRIPTION

GiA Roots is a software package designed to assist in the high-throughput analysis of root system architecture.

::DEVELOPER

the Weitz group at Georgia Tech, the Harer group at Duke University and the Benfey laboratory at Duke University.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 GiA Roots

:: MORE INFORMATION

Citation:

Galkovskyi, T, Mileyko, Y., Bucksch, A., Moore, B., Symonova, O., Price, C.A., Topp, C.N., Iyer-Pascuzzi, A.S., Zurek, P.R., Fang, S., Harer, J., Benfey, P.N. and Weitz, J.S. (2012)
GiA Roots: software for the high-throughput analysis of plant root system architecture.
BMC Plant Biology. 12:116.