GEMSiRV 20130911 – GEnome-scale Metabolic Model Simulation, Reconstruction and Visualization

GEMSiRV 20130911

:: DESCRIPTION

GEMSiRV is a software platform to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies.

::DEVELOPER

GEMSiRV team

:: SCREENSHOTS

GEMSiRV

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 GEMSiRV

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.
Liao YC1, Tsai MH, Chen FC, Hsiung CA.

GenPlay 1.1.0 – Genome Analyzer and Browser

GenPlay 1.1.0

:: DESCRIPTION

GenPlay is an analyzer and browser for high-throughput data . GenPlay recognizes a wide variety of common genomic data formats from microarray- or sequencing-based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualizable tracks.

::DEVELOPER

Eric Bouhassira, Nicolas Fourel and Julien Lajugie

:: SCREENSHOTS

GenPlay1

GenPlay

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  GenPlay

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Aug 31. pii: btu588.
GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.
Lajugie J, Fourel N, Bouhassira EE

Bioinformatics. 2011 Jul 15;27(14):1889-93.
GenPlay, a multipurpose genome analyzer and browser.
Lajugie J, Bouhassira EE.

DeepDRBP-2L – Genome Annotation predictor for identifying DNA-binding proteins and RNA-binding proteins

DeepDRBP-2L

:: DESCRIPTION

DeepDRBP-2L is a new computational predictor for identifying DBPs, RBPs and DRBPs by combining Convolutional Neural Network (CNN) and the Long Short-Term Memory (LSTM).

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Zhang J, Chen Q, Liu B.
DeepDRBP-2L: A New Genome Annotation Predictor for Identifying DNA-Binding Proteins and RNA-Binding Proteins Using Convolutional Neural Network and Long Short-Term Memory.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul-Aug;18(4):1451-1463. doi: 10.1109/TCBB.2019.2952338. Epub 2021 Aug 6. PMID: 31722485.

airpg 1.1.4 – Automatically Accessing the inverted Repeats of Archived Plastid Genomes

airpg 1.1.4

:: DESCRIPTION

airpg is an Python package for automatically accessing the inverted repeats of thousands of plastid genomes stored on NCBI Nucleotide

::DEVELOPER

Michael Gruenstaeudl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOs
  • Python

:: DOWNLOAD

airpg

:: MORE INFORMATION

Citation

Mehl T, Gruenstaeudl M.
airpg: automatically accessing the inverted repeats of archived plastid genomes.
BMC Bioinformatics. 2021 Aug 21;22(1):413. doi: 10.1186/s12859-021-04309-y. PMID: 34418956; PMCID: PMC8379869.

miRNAFold – Ab initio miRNA Precursor Search in Genomes

miRNAFold

:: DESCRIPTION

miRNAFold is a fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRNAFold: a web server for fast miRNA precursor prediction in genomes.
Tav C, Tempel S, Poligny L, Tahi F.
Nucleic Acids Res. 2016 May 29. pii: gkw459.

Nucleic Acids Res. 2012 Jun;40(11):e80. doi: 10.1093/nar/gks146. Epub 2012 Feb 22.
A fast ab-initio method for predicting miRNA precursors in genomes.
Tempel S1, Tahi F.

Geptop 2.0 – Gene Essentiality Prediction tool for COMPLETE-GENOME based on Orthology and Phylogeny

Geptop 2.0

:: DESCRIPTION

Geptop is a webserver, which first provides a platform to detect essential gene sets over bacterial species, by comparing orthology and phylogeny of query protein sets with essential gene datasets determined experimentally (from DEG database).

::DEVELOPER

Microbe and Drug Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Python
  • BioPython

:: DOWNLOAD

 Geptop

:: MORE INFORMATION

Citation

PLoS One. 2013 Aug 15;8(8):e72343. doi: 10.1371/journal.pone.0072343. eCollection 2013.
Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny.
Wei W1, Ning LW, Ye YN, Guo FB.

MaGnET 2.0 – Malaria Genome Exploration Tool

MaGnET 2.0

:: DESCRIPTION

MaGnET is a software tool enabling intuitive ‘exploration-style’ visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum.

::DEVELOPER

MaGnET team

:: SCREENSHOTS

MaGnET

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 MaGnET

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Sep 15;29(18):2350-2. doi: 10.1093/bioinformatics/btt384. Epub 2013 Jul 27.
MaGnET: Malaria Genome Exploration Tool.
Sharman JL1, Gerloff DL.

L_RNA_scaffolder – Long Transcriptome Reads to Scaffold Genome

L_RNA_scaffolder

:: DESCRIPTION

L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments.

::DEVELOPER

L_RNA_scaffolder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Perl

:: DOWNLOAD

 L_RNA_scaffolder

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 Sep 8;14:604. doi: 10.1186/1471-2164-14-604.
L_RNA_scaffolder: scaffolding genomes with transcripts.
Xue W1, Li JT, Zhu YP, Hou GY, Kong XF, Kuang YY, Sun XW.

DNAcompact 20130829 – Genome Compression algorithm with/without Reference

DNAcompact 20130829

:: DESCRIPTION

DNA-COMPACT is a software of DNA COMpression based on a pattern-aware contextual modeling technique.

::DEVELOPER

DNAcompact team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 DNAcompact

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 25;8(11):e80377. doi: 10.1371/journal.pone.0080377. eCollection 2013.
DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique.
Li P1, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X.

AutoEditor 1.20 – Automated Correction of Genome Sequence Errors

AutoEditor 1.20

:: DESCRIPTION

AutoEditor is a tool for correcting sequencing and basecaller errors using sequence assembly and chromatogram data. On average AutoEditor corrects 80% of erroneous base calls, with an accuracy of 99.99%.This in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AutoEditor

:: MORE INFORMATION

Citation

“Automated correction of genome sequence errors.”
Gajer P, Schatz M, Salzberg SL,
Nucleic Acids Research, 2004. 32(2):562-9.