FRODOCK 3.12 – Fast Rotational DOCKing tool

FRODOCK 3.12

:: DESCRIPTION

FRODOCK is able to generates very efficiently many potential predictions of how  two proteins could interact. This approximation effectively address the complexity and sampling requirements of the initial 6D docking exhaustive search by combining the projection of the interaction terms into 3D grid-based potentials with the efficiency of spherical harmonics approximations. The binding energy upon complex formation is approximated as a correlation function composed of van der Waals, electrostatics and desolvation potential terms. This initial stage exhaustive docking obtain excellent accuracy results with standard benchmarks, thus you can use it directly as a first protein-protein rigid-body docking approach.

::DEVELOPER

The Structural Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

  FRODOCK

:: MORE INFORMATION

Citation

J. I. Garzon, J. R. Lopéz-Blanco, C. Pons, J. Kovacs, R. Abagyan, J. Fernandez-Recio, P. Chacón (2009)
FRODOCK: a new approach for fast rotational protein-protein docking
Bioinformatics, 25, 2544-2551

YASS 1.15 – Genomic Similarity Search Tool

YASS 1.15

:: DESCRIPTION

YASS  (Yet Another Similarity Searcher) is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments).  Like most of the heuristic DNA local alignment software (BLAST, FASTA, PATTERNHUNTER, BLASTZ …), YASS uses seeds to detect potential similarity regions, and then tries to extend them to actual alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step

YASS Online Version

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 YASS

:: MORE INFORMATION

Citation

L. Noe, G. Kucherov,
YASS: enhancing the sensitivity of DNA similarity search, 2005,
Nucleic Acids Research, 33(2):W540-W543.

eRNA 1.01 – RNA Data Analysis Tool

eRNA 1.01

:: DESCRIPTION

eRNA is an RNA data analysis tool for high-throughput RNA sequencing experiments

::DEVELOPER

eRNA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • Perl
  • R

:: DOWNLOAD

 eRNA 

:: MORE INFORMATION

Citation:

BMC Genomics. 2014 Mar 5;15:176. doi: 10.1186/1471-2164-15-176.
eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.
Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, Thibodeau SN, Wang L

PSI-BLAST-ISS 1.04 – The PSI-BLAST Intermediate Sequence Search tool

PSI-BLAST-ISS 1.04

:: DESCRIPTION

PSI-BLAST-ISS is a standalone Unix-based tool designed to delineate reliable regions of sequence alignments as well as to suggest potential variants in unreliable regions. The region-specific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of alignment variants. The PSI-BLAST-ISS output enables the user to simultaneously analyze alignment reliability between query and multiple homologous sequences. In addition, PSI-BLAST-ISS can be used to detect distantly related homologous proteins.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 PSI-BLAST-ISS

:: MORE INFORMATION

Citation

Margelevicius M., Venclovas C. (2005)
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability.
BMC Bioinformatics 6(1):185

CPAT 2.0.0 – RNA Coding Potential Assessment Tool

CPAT 2.0.0

:: DESCRIPTION

CPAT (Coding Potential Assessment Tool) is a novel alignment-free method which rapidly recognizes coding and noncoding transcripts from a large pool of candidates.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • R package

:: DOWNLOAD

 CPAT

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Apr 1;41(6):e74. doi: 10.1093/nar/gkt006. Epub 2013 Jan 17.
CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.
Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W.

ABMapper 2.0.4 – A suffix-array based Spliced Alignment tool

ABMapper 2.0.4

:: DESCRIPTION

ABMapper is a portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping.

::DEVELOPER

ABMapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Perl

:: DOWNLOAD

  ABMapper

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):421-2. doi: 10.1093/bioinformatics/btq656. Epub 2010 Dec 17.
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.
Lou SK, Ni B, Lo LY, Tsui SK, Chan TF, Leung KS.

TopKCEMC 1.1 / TopKSpace 1.0 – Rank Aggregation Tool

TopKCEMC 1.1 / TopKSpace 1.0

:: DESCRIPTION

TopKCEMC is a rank aggregation tool for integrating data from multiple sources based on ranks.

TopKSpace: based on Borda’s and Markov chain methods that take spaces from the which the individual ranked lists are derived into consideration

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R package

:: DOWNLOAD

 TopKCEMC , TopKSpace

:: MORE INFORMATION

Citation

Lin, S., Ding, J. (2009)
Integration of Ranked Lists via Cross Entropy Monte Carlo with Applications to mRNA and microRNA Studies.
Biometrics, 65, 9-18

Lin, S. (2010)
Space oriented rank-based data integration.
Statistical Applications in Genetics and Molecular Biolog, 20, Article 20.

Blast2GO 5.2.5 – Functional Annotation Tool

Blast2GO 5.2.5

:: DESCRIPTION

Blast2GO® is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Blast2GO

:: MORE INFORMATION

Citation

A. Conesa, S. Götz, J. M. Garcia-Gomez, J. Terol, M. Talon and M. Robles.
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research“,
Bioinformatics, Vol. 21, September, 2005, pp. 3674-3676.

JADOPPT – Java based AutoDock Preparing and Processing Tool

JADOPPT

:: DESCRIPTION

JADOPPT is a tool for automatically preparing and processing multiple AutoDock results, thus allowing their simultaneous analysis and comparison.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux /MacOs
  • Java

:: DOWNLOAD

JADOPPT

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):583-585. doi: 10.1093/bioinformatics/btw677.
JADOPPT: java based AutoDock preparing and processing tool.
García-Pérez C, Peláez R, Therón R, Luis López-Pérez J.

SmashCommunity 1.6p2 – Metagenomic Analysis and Annotation Tool

SmashCommunity 1.6p2

:: DESCRIPTION

 SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It comes with built-in support for state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction, and can be easily extended to support additional software. SmashCommunity provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, compare compositions of multiple metagenomes and produce intuitive visual representations of such analyses.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SmashCommunity

:: MORE INFORMATION

Citation

Arumugam, M., Harrington, E. D., Foerstner, K. U., Raes, J. and P. Bork. (2010)
SmashCommunity: A metagenomic annotation and analysis tool,
Bioinformatics, 26, 2977-8.