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

iDoComp 1.1 – Compression Scheme for Assembled Genomes

iDoComp 1.1

:: 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

Idoia Ochoa-Alvarez ,  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.

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 <torsten.seemann@monash.edu>,Victorian Bioinformatics Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 VelvetK

:: MORE INFORMATION

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

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

Kevin Teague

:: 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

AmosCmp16Spipeline 20090918 – Assemble 16S rRNA Sequencing Reads

AmosCmp16Spipeline 20090918

:: DESCRIPTION

AmosCmp16Spipeline uses the AMOScmp software to assemble multiple, potentially overlapping 16S rRNA sequencing reads based on read mappings to a reference 16S rRNA gene.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AmosCmp16Spipeline

:: MORE INFORMATION

Citation

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW.
Genome Res. 2011 Mar;21(3):494-504. Epub 2011 Jan 6.