PEAssember 1.2 – A de novo Genome Assembler

PEAssember 1.2

:: DESCRIPTION

PEAssember is a parallel de novo genome assembler for small – mid sized genomes.

::DEVELOPER

Pramila Nuwantha Ariyaratne, Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • C++ Compiler

:: DOWNLOAD

 PEAssember

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):167-74. doi: 10.1093/bioinformatics/btq626. Epub 2010 Dec 12.
PE-Assembler: de novo assembler using short paired-end reads.
Ariyaratne PN, Sung WK.

SEME 1.0 – A de novo Motif Finder for ChIP-seq data

SEME 1.0

:: DESCRIPTION

SEME ( Sampling with Expectation maximization for Motif Elicitation) is a de novo motif discovery algorithm  which uses pure probabilistic mixture model to model the motif’s binding features and uses expectation maximization (EM) algorithms to simultaneously learn the sequence motif, position, and sequence rank preferences without asking for any prior knowledge from the user.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 SEME 

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Mar;20(3):237-48. doi: 10.1089/cmb.2012.0233.
Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm.
Zhang Z, Chang CW, Hugo W, Cheung E, Sung WK.

Dimont – de-novo Motif Discovery tool

Dimont

:: DESCRIPTION

Dimont is a universal tool for de-novo motif discovery. Dimont has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.

::DEVELOPER

Jstacs Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 Dimont

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Nov;41(21):e197. doi: 10.1093/nar/gkt831. Epub 2013 Sep 20.
A general approach for discriminative de novo motif discovery from high-throughput data.
Grau J1, Posch S, Grosse I, Keilwagen J.

SSP – de novo Transcriptome Assembler

SSP

:: DESCRIPTION

SSP is a de novo transcriptome assembler that assembles RNA-seq reads into transcripts. SSP aims to reconstructs all the alternatively spliced isoforms and estimates the expression level of them.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux

:: DOWNLOAD

 SSP

:: MORE INFORMATION

GibbsModule – Multispecies de novo Identification of Cis-regulatory Motifs and Modules

GibbsModule

:: DESCRIPTION

GibbsModule is a software for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the coexpressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 GibbsModule

:: MORE INFORMATION

Citation

Genome Res. 2008 Aug;18(8):1325-35. Epub 2008 May 15.
Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.
Xie D, Cai J, Chia NY, Ng HH, Zhong S.

Rnnotator 3.5.0 – de novo Transcriptome Assembly pipeline from stranded RNA-Seq reads

Rnnotator 3.5.0

:: DESCRIPTION

Rnnotator is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome.

::DEVELOPER

Zhong Wang at U.S. Department of Energy Joint Genome Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BioPerl
  • Blat

:: DOWNLOAD

  Rnnotator

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Nov 24;11:663. doi: 10.1186/1471-2164-11-663.
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Martin J, Bruno VM, Fang Z, Meng X, Blow M, Zhang T, Sherlock G, Snyder M, Wang Z.

RIPSeeker 1.26.0 – de novo RIP Peak Predictions based on HMM.

RIPSeeker 1.26.0

:: DESCRIPTION

RIPSeeker is a free open-source Bioconductor/R package for identifying protein-associated transcripts from RIP-seq experiments.

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 RIPSeeker

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Apr;41(8):e94. doi: 10.1093/nar/gkt142. Epub 2013 Feb 28.
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.
Li Y1, Zhao DY, Greenblatt JF, Zhang Z.

HHrepID 1.0.0 – de novo Protein Repeat Detection

HHrepID 1.0.0

:: DESCRIPTION

HHrepID is a novel automated procedure for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as TIM barrels and outer membrane beta-barrels. HHrepID uses HMM-HMM comparison to exploit evolutionary information in the form of the multiple sequence alignment of homologs, but in contrast to HHrep, the new method has several novel characteristics: (1) automated generation of a multiple alignment of repeats; (2) utilization of the transitive nature of homology through a novel merging procedure based on the fully probabilistic treatment of alignments; (3) superior alignment quality through an algorithm that maximizes the expected accuracy of an alignment; (4) the ability to identify different repeats within complicated architectures or multiple domains through automatic domain boundary detection, (5) new statistical treatment yielding improved sensitivity.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  HHrepID

:: MORE INFORMATION

Citation

Biegert A, Söding J:
HHrepID: de novo protein repeat identification by probabilistic consistency
Bioinformatics 2008 24(6), 807-814.

MAP 20121108 – A de novo Metagenomic Assembly program for Shotgun DNA reads

MAP 20121108

:: DESCRIPTION

MAP (Metagenomic Assembly program) is a de novo assembly approach and its implementation based on an improved Overlap/Layout/Consensus (OLC) strategy incorporated with several special algorithms.MAP uses the mate pair information, resulting in being more applicable to shotgun DNA reads (recommended as > 200 bp) currently widely-used in metagenome projects. Results of extensive tests on simulated data show that MAP can be superior to both Celera and Phrap for typical longer reads by Sanger sequencing, as well as has an evident advantage over Celera, Newbler, and the newest Genovo, for typical shorter reads by 454 sequencing.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MAP

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1455-62. Epub 2012 Apr 11.
A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.