Category: DNA / Genome Analysis

ChemGenome 2.1 – Gene Prediction Software

ChemGenome 2.1

:: DESCRIPTION

Chemgenome is an ab-intio gene prediction software, which find genes in prokaryotic genomes in all six reading frames. The methodology follows a physico-chemical approach and has been validated on 372 prokaryotic genomes.

::DEVELOPER

Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ChemGenome

:: MORE INFORMATION

Citation:

PLoS One. 2010 Aug 26;5(8):e12433.
A phenomenological model for predicting melting temperatures of DNA sequences.
Khandelwal G, Bhyravabhotla J.

MOSGA 2 – Modular Open-Source Genome Annotator

MOSGA 2

:: DESCRIPTION

The MOSGA is a pipeline that easily creates draft genome annotation by a graphical user interface. It combines several specific prediction tools and generates a submission-ready annotation file.

::DEVELOPER

MOSGA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MOSGA

:: MORE INFORMATION

Citation

Martin R, Hackl T, Hattab G, Fischer MG, Heider D.
MOSGA: Modular Open-Source Genome Annotator.
Bioinformatics. 2021 Apr 1;36(22-23):5514-5515. doi: 10.1093/bioinformatics/btaa1003. PMID: 33258916.

Martin R, Dreßler H, Hattab G, Hackl T, Fischer MG, Heider D.
MOSGA 2: Comparative genomics and validation tools.
Comput Struct Biotechnol J. 2021 Sep 28;19:5504-5509. doi: 10.1016/j.csbj.2021.09.024. PMID: 34712396; PMCID: PMC8517542.

 

Genome Workbench 3.7.1 – View & Analyze Sequence Data

Genome Workbench 3.7.1

:: DESCRIPTION

Gbench (NCBI Genome Workbench) is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

::DEVELOPER

Genome Workbench Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

Genome Workbench

:: MORE INFORMATION

Genoogle BETA 0.81 – Fast similar DNA sequence Searching Engine

Genoogle BETA 0.81

:: DESCRIPTION

Genoogle is a software for fast similar DNA sequence searching. It is a full functional similar genetics searching tool, having a text mode interface with simple scripting language, web interface, and web service interface.

::DEVELOPER

Felipe Albrecht

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

 Genoogle

:: MORE INFORMATION

nFuse 0.2.1 – Discovery of Complex Genomic Rearrangements in Cancer

nFuse 0.2.1

:: DESCRIPTION

nFuse is a tool for detecting fusion transcripts and associated complex genomic rearrangements from matched RNA-seq and whole genome shotgun sequencing.nFuse predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

::DEVELOPER

Andrew McPherson (andrew.mcpherson@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 nFuse

:: MORE INFORMATION

Citation:

McPherson AW, Wu C, Wyatt A, Shah SP, Collins C, Sahinalp SC.
nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
Genome Res. 2012 Jun 28.

DECOD 1.0.1 – Fast and Accurate Discriminative Motif Finding

DECOD 1.0.1

:: DESCRIPTION

DECOD (DECOnvolved Discriminative) is a tool for finding discriminative DNA motifs, i.e. motifs that are over-represented in one set of sequences but are depleted from another.

::DEVELOPER

DECOD team

:: SCREENSHOTS

DECOD

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 DECOD

:: MORE INFORMATION

Citation

DECOD: fast and accurate discriminative DNA motif finding.
Huggins P, Zhong S, Shiff I, Beckerman R, Laptenko O, Prives C, Schulz MH, Simon I, Bar-Joseph Z.
Bioinformatics. 2011 Sep 1;27(17):2361-7. doi: 10.1093/bioinformatics/btr412.

TinT – Screening for Nested Transpositions from Genome Assemblies or Trace data

TinT

:: DESCRIPTION

TinT (Transposition in Transposition) affords an easy, automated screening for nested transpositions from genome assemblies or trace data, assembles them in a frequency-matrix, and schematically displays their chronological activity history

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Window / MacOsX
  • Java

:: DOWNLOAD

 TinT

:: MORE INFORMATION

Citation

Churakov G, Grundmann N, Kuritzin A, Brosius J, Makalowski W, Schmitz J. (2010)
A Novel Web-Based TinT Application and the Chronology of the Primate Alu Retroposon Activity.
BMC Evolutionary Biology 10:376.

SCA – Sequence Composition Analysis

SCA

:: DESCRIPTION

The SCA (sequence composition analysis) takes a set of sequences in fasta format and generates a 2-dimensional crossed graph displaying the value of a given formula on the x-axis against the year of the sequences on the y-axis. The year is taken from the header line of each source sequence (starting with “>”). Additionally the points may be colored depending of the host the sequence is taken from.

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 SCA

:: MORE INFORMATION

DistG – Distribution Graph

DistG

:: DESCRIPTION

DistG counts the length of fasta sequences and make a graphical representation about. There are two king of graphs. The first is the distribution graph, giving an overview of all read fasta files (sequences) so far. The second graph displays a specific file’s counting as a set of rectangles.

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 DistG

:: MORE INFORMATION