Tag: Ribosomal

ProteoVision – Advanced Visualization of (Ribosomal) Proteins

ProteoVision

:: DESCRIPTION

ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures.

::DEVELOPER

ProteoVision team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Penev PI, McCann HM, Meade CD, Alvarez-Carreño C, Maddala A, Bernier CR, Chivukula VL, Ahmad M, Gulen B, Sharma A, Williams LD, Petrov AS.
ProteoVision: web server for advanced visualization of ribosomal proteins.
Nucleic Acids Res. 2021 Jul 2;49(W1):W578-W588. doi: 10.1093/nar/gkab351. PMID: 33999189; PMCID: PMC8265156.

REAGO 1.1 – REconstruct 16S ribosomal RNA Genes from MetagenOmic data

REAGO 1.1

:: DESCRIPTION

REAGO is an assembly tool for 16S ribosomal RNA recovery from metagenomic data

::DEVELOPER

Cheng Yuan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 REAGO

:: MORE INFORMATION

Citation

Reconstructing 16S rRNA genes in metagenomic data.
Yuan C, Lei J, Cole J, Sun Y.
Bioinformatics. 2015 Jun 15;31(12):i35-i43. doi: 10.1093/bioinformatics/btv231.

RNAmmer 1.2 – Ribosomal RNA Sub Units

RNAmmer 1.2

:: DESCRIPTION

RNAmmer  predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RNAmmer

:: MORE INFORMATION

Citation

RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Stærfeldt, Torbjørn Rognes and David W. Ussery
Nucl. Acids Res. (2007) 35 (9): 3100-3108

ITSx 1.1.3 – Extraction of ITS1 and ITS2 from Ribosomal ITS Sequences

ITSx 1.1.3

:: DESCRIPTION

ITSx is a software tool for detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing.

::DEVELOPER

The Bengtsson-Palme Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 ITSx

:: MORE INFORMATION

Citation:

ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
Johan Bengtsson-Palme, Vilmar Veldre, Martin Ryberg, Martin Hartmann, Sara Branco, Zheng Wang, Anna Godhe, Yann Bertrand, Pierre De Wit, Marisol Sanchez, Ingo Ebersberger, Kemal Sanli, Filipe de Souza, Erik Kristiansson, Kessy Abarenkov, K. Martin Eriksson, R. Henrik Nilsson
Methods in Ecology and Evolution, 2013

Megraft 1.0.2 – Graft Ribosomal Small Subunit (16S/18S) Fragments onto full-length SSU Sequences

Megraft 1.0.2

:: DESCRIPTION

Megraft is a software package that grafts SSU (small subunit) fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.

::DEVELOPER

The Bengtsson-Palme Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Megraft

:: MORE INFORMATION

Citation:

Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21.
Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.
Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson R