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

ASAP – Assemble Species by Automatic Partitioning

ASAP

:: DESCRIPTION

ASAP is a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets).

::DEVELOPER

L’Atelier de BioInformatique

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Puillandre N, Brouillet S, Achaz G.
ASAP: assemble species by automatic partitioning.
Mol Ecol Resour. 2021 Feb;21(2):609-620. doi: 10.1111/1755-0998.13281. Epub 2020 Nov 20. PMID: 33058550.

VelvetK 20120606 – Find a reasonable K-mer size to Assemble Genome Reads with Velvet

VelvetK 20120606

:: DESCRIPTION

VelvetK can estimate the best k-mer size to use for your Velvet de novo assembly. It needs two inputs: the estimated genome size, and all your sequence read files. The genome size can be supplied as as a number (eg. 3.5M) or as a FASTA file of a closely related genome.

::DEVELOPER

Torsten Seemann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

VelvetK

:: MORE INFORMATION

THOR 1.0 – Assemble Target Genomic Sequence Orthologs

THOR 1.0

:: DESCRIPTION

THOR (Targeted High-throughput Ortholog Reconstructor) is a Java application designed to assemble target genomic sequence orthologs in low-coverage genomes.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
Java

:: DOWNLOAD

THOR

:: MORE INFORMATION

Citation

Matthew N. Bainbridge* René L. Warren, An He, Mikhail Bilenky, A. Gordon Robertson and Steven J.M. Jones
THOR: targeted high-throughput ortholog reconstructor
Bioinformatics (2007) 23 (19): 2622-2624

iDoComp 1.2 – Compression Scheme for Assembled Genomes

iDoComp 1.2

:: DESCRIPTION

iDoComp is an algorithm to compress re-sequenced assembled genomes, i.e., genomes for which an assembled genome of the same species already exists

::DEVELOPER

Mikel Hernaez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
C Compiler

:: DOWNLOAD

iDoComp

:: MORE INFORMATION

Citation

iDoComp: A Compression Scheme for Assembled Genomes.
Ochoa I, Hernaez M, Weissman T.
Bioinformatics. 2014 Oct 24. pii: btu698.

SequenceAssembly 20111004 – Assemble Amino Acid Sequences of Entire Proteins

SequenceAssembly 20111004

:: DESCRIPTION

SequenceAssembly is a program to assemble amino acid sequences of entire proteins

::DEVELOPER

The Mass Spectrometry Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

SequenceAssembly

:: MORE INFORMATION