DISSECT 1.0.2 – Transcriptome-to-Genome Alignment Tool

DISSECT 1.0.2

:: DESCRIPTION

Dissect (DIScovery of Structural Alteration Event Containing Transcripts) is a transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. Dissect is suitable for whole transcriptome structural variation discovery problems involving sufficiently long reads or accurately assembled contigs.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  DISSECT

:: MORE INFORMATION

Citation

Yorukoglu D, Hach F, Swanson L, Collins CC, Birol I, Sahinalp SC
Dissect: detection and characterization of novel structural alterations in transcribed sequences
Bioinformatics. 2012 Jun 15;28(12):i179-87

Sibelia 3.0.7 – Synteny Block ExpLoration tool

Sibelia 3.0.7

:: DESCRIPTION

Sibelia is a comparative genomic tool。 It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments.

::DEVELOPER

Algorithmic Biology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Windows

:: DOWNLOAD

 Sibelia

:: MORE INFORMATION

Citation

F1000Res. 2013 Nov 25;2:258. doi: 10.12688/f1000research.2-258.v1. eCollection 2013.
C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison.
Minkin I, Pham H, Starostina E, Vyahhi N, Pham S

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham.
Sibelia: A fast synteny blocks generation tool for many closely related microbial genomes
(submitted)

OptiMAS 1.5 – Decision Support tool to conduct Marker-Assisted Selection programs

OptiMAS 1.5

:: DESCRIPTION

OptiMAS has been developed with the possibility to consider a multi-allelic context,which opens new prospects to further accelerate genetic gain by assembling favorable alleles issued from diverse parents.

:: DEVELOPER

ABI Bioinformatic and Informatic Team 

:: SCREENSHOTS

OptiMAS

:: REQUIREMENTS

  •  Windows / Linux / MacOsX

:: DOWNLOAD

 OptiMAS

:: MORE INFORMATION

Citation:

Valente, F., Gauthier, F., Bardol, N., Blanc, G., Joets, J., Charcosset, A. & Moreau, L. (in prep)
OptiMAS: decision support for marker-assisted selection.

PGDSpider 2.1.1.5 – Data conversion tool for Population Genetic and Genomics Programs

PGDSpider 2.1.1.5

:: DESCRIPTION

PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances).

::DEVELOPER

Computational and Molecular Population Genetics Lab, University of Bern

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX / Linux
  • java

:: DOWNLOAD

 PGDSpider

:: MORE INFORMATION

Citation

Lischer HEL and Excoffier L (2012)
PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs.
Bioinformatics 28: 298-299.

cERMIT v1.2 – the Evidence Ranked Motif Identification Tool

cERMIT v1.2

:: DESCRIPTION

cERMIT is a computationally efficient motif discovery tool based on analyzing genome-wide quantitative regulatory evidence.

::DEVELOPER

Uwe Ohler’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

  cERMIT

:: MORE INFORMATION

Citation:

Genome Biol. 2010;11(2):R19. doi: 10.1186/gb-2010-11-2-r19. Epub 2010 Feb 15.
Evidence-ranked motif identification.
Georgiev S, Boyle AP, Jayasurya K, Ding X, Mukherjee S, Ohler U.

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

eRNA

:: 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.