Tag: Assignment

NASCA 20110516 – Side-chain Resonance Assignment & NOE Assignment

NASCA 20110516

:: DESCRIPTION

NASCA (NOE Assignment and Side-Chain Assignment) is an automated program for side-chain resonance assignment and nuclear Overhauser effect (NOE) assignment from NOESY data. It does not require data from TOCSY experiments.NASCA casts the assignment problem into a Markov Random Field (MRF), and extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

NASCA

:: MORE INFORMATION

Citation

Jianyang Zeng, Pei Zhou, Bruce R. Donald.
Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data.
J Biomol NMR. 2011 Aug;50(4):371-95. doi: 10.1007/s10858-011-9522-4.

RDC-PANDA 1.0 – NMR NOE Assignment & Protein Structure Determination

RDC-PANDA 1.0

:: DESCRIPTION

RDC-PANDA (RDC-based SSE PAcking with NOEs for Structure Determination and NOE Assignment) is a suite of programs for nuclear Overhauser effect (NOE) assignment and high-resolution structure determination starting with a global fold calculated from exact solutions to the residual dipolar coupling (RDC) equations. RDC-PANDA is specifically designed for automated NMR NOE assignment and protein structure determination.

::DEVELOPER

Donald Lab at Duke University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

RDC-PANDA

:: MORE INFORMATION

Citation

Jianyang Zeng, Jeffrey Boyles, Chittaranjan Tripathy, Lincong Wang, Anthony Yan, Pei Zhou, and Bruce Randall Donald.
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.
Journal of Biomolecular NMR, 45(3):265-281, 2009

PARma 1.0 – PAR-CLIP data microRNA Assignment

PARma 1.0

:: DESCRIPTION

PAR-CLIP is a high-throughput method to identify binding sites of RNA binding proteins.

::DEVELOPER

Institute for Bioinformatics, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 PAR-CLIP

:: MORE INFORMATION

Citation

PARma: identification of microRNA target sites in Argonaute PAR-CLIP data.
Erhard F, Dolken L, Jaskiewicz L, Zimmer R.
Genome Biol. 2013 Jul 29;14(7):R79.
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MARS 1.2 – Robust Automatic Backbone Assignment of Proteins

MARS 1.2

:: DESCRIPTION

MARS is a program for robust automatic backbone assignment of 13C/15N labeled proteins. It can be applied independent of the assignment complexity, it does not require tight thresholds for establishing sequential connectivity or detailed adjustment of these thresholds, it can work with a wide variety of NMR experiments and it is robust against missing chemical shift information. In case of a known 3D structure, residual dipolar couplings can be used to enhance assignment.

::DEVELOPER

Research Group Zweckstetter

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX

:: DOWNLOAD

  MARS

:: MORE INFORMATION

Citation

Mars — robust automatic backbone assignment of proteins.
Jung YS, Zweckstetter M.
J Biomol NMR. 2004 Sep;30(1):11-23.

cellassign v0.99.2 – Automated, Probabilistic Assignment of Cell Types in scRNA-seq data

cellassign v0.99.2

:: DESCRIPTION

cellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

cellassign

:: MORE INFORMATION

Citation

Zhang AW, etc.
Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling,
Nat Methods. 2019 Oct;16(10):1007-1015. doi: 10.1038/s41592-019-0529-1.

taxator-tk 1.3.3 – Taxonomic Sequence Assignment

taxator-tk 1.3.3

:: DESCRIPTION

taxator-tk is an algorithm and the accompanying software, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities.

::DEVELOPER

Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 taxator-tk

:: MORE INFORMATION

Citation

Taxator-tk: Precise Taxonomic Assignment of Metagenomes by Fast Approximation of Evolutionary Neighborhoods.
Dröge J, Gregor I, McHardy AC.
Bioinformatics. 2014 Nov 10. pii: btu745.

STRIDE – Secondary Structure Assignment from known Atomic Coordinates of Proteins

STRIDE

:: DESCRIPTION

STRIDE conduct the secondary structure assignment from atomic resolution protein structures.

::DEVELOPER

the Dmitrij Frishman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 STRIDE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W500-2.
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins.
Heinig M1, Frishman D.

COMPASS 2.01 – Protein Backbone Resonance Assignment

COMPASS 2.01

:: DESCRIPTION

COMPASS is used for protein backbone resonance assignment from unassigned triple resonance peak lists. Compared to most other software for the same purpose, COMPASS lets the user control the assignment process, enabling supreme accuracy. COMPASS is well suited for the assignment of larger deuterated proteins.

::DEVELOPER

Patrik Lundström

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 COMPASS

:: MORE INFORMATION

Citation

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.
Niklasson M, Ahlner A, Andresen C, Marsh JA, Lundström P.
PLoS Comput Biol. 2015 Jan 8;11(1):e1004022. doi: 10.1371/journal.pcbi.1004022.

PhosSA – Phosphorylation Site Assignment Algorithm for Mass Spectrometry Data

PhosSA

:: DESCRIPTION

PhosSA is a program for phosphorylation site assignment of LC-MS/MS data. It uses a linear-time and linear space dynamic programming strategy for phosphorylation site assignment. The algorithm optimizes the objective function defined as the summation of intensity peaks that are associated with theoretical peptide fragmentation ions. A classifier introduced in the algorithm exploits the specific characteristics of mass spectrometry data to distinguish between the correctly and incorrectly assigned site(s).

::DEVELOPER

Epithelial Systems Biology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • JRE

:: DOWNLOAD

PhosSA

:: MORE INFORMATION

Citation

Proteome Sci. 2013 Nov 7;11(Suppl 1):S14. doi: 10.1186/1477-5956-11-S1-S14. Epub 2013 Nov 7.
PhosSA: Fast and accurate phosphorylation site assignment algorithm for mass spectrometry data.
Saeed F, Pisitkun T, Hoffert JD, Rashidian S, Wang G, Gucek M, Knepper MA.

BAM_ABS – Bayesian Assignment Method for Ambiguous Bisulfite Short Reads

BAM-ABS

:: DESCRIPTION

BAM_ABS is a tool which simulates a Bayesian model that computes the posterior probability of mapping a multiread to each candidate genomic location, taking advantage of uniquely aligned reads.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

BAM_ABS

:: MORE INFORMATION

Citation

Tran H, Wu X, Tithi S, Sun MA, Xie H, Zhang L.
A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads.
PLoS One. 2016 Mar 24;11(3):e0151826. doi: 10.1371/journal.pone.0151826. PMID: 27011215; PMCID: PMC4806927.

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