motif-x 1.2 – Biological Sequence Motif Discovery

motif-x 1.2

:: DESCRIPTION

motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.

::DEVELOPER

Schwartz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2011 Sep;Chapter 13:Unit 13.15-24. doi: 10.1002/0471250953.bi1315s35.
Biological sequence motif discovery using motif-x.
Chou MF, Schwartz D.

MetaCompass v2.0-beta – Reference-guided Assembly of Metagenomes

MetaCompass v2.0-beta

:: DESCRIPTION

MetaCompass represents the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MetaCompass

:: MORE INFORMATION

MetaCarvel v1.1 – A Scaffolder for Metagenomes

MetaCarvel v1.1

:: DESCRIPTION

MetaCarvel is an updated version of previous metagenome scaffolder Bambus 2.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MetaCarvel

:: MORE INFORMATION

Citation:

Ghurye, J., Treangen, T., Fedarko, M., Hervey, W. J., & Pop, M. (2019).
MetaCarvel: linking assembly graph motifs to biological variants.
Genome biology, 20(1), 1-14.

Mash v2.2 – Fast Similarity Estimates via MinHash

Mash v2.2

:: DESCRIPTION

Mash is a software of fast genome and metagenome distance estimation using MinHash

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

Mash

:: MORE INFORMATION

Citation:

Genome Biol, 17 (1), 132
Mash: Fast Genome and Metagenome Distance Estimation Using MinHash
Brian D Ondov , Todd J Treangen , Páll Melsted , Adam B Mallonee , Nicholas H Bergman , Sergey Koren , Adam M Phillippy

MetaPhyler 1.25 – Taxonomic Profiling for Metagenomic Sequences

MetaPhyler 1.25

:: DESCRIPTION

MetaPhyler is a novel taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. Our classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. Our reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. Results on simulated metagenomic datasets demonstrate that MetaPhyler outperforms previous tools used in this context (CARMA, MEGAN and PhymmBL).

::DEVELOPER

Bo Liu 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MetaPhyler

:: MORE INFORMATION

Citation:

BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.

iMotifs 0.2.5 – Sequence Motif Editor for the Mac

iMotifs 0.2.5

:: DESCRIPTION

iMotifs is a graphical motif analysis environment for the Apple Mac computers (Leopard or later).It allows visualization of annotated sequence motifs and scored motif hits in sequences.

::DEVELOPER

iMotifs team

:: SCREENSHOTS

iMotifs

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

 iMotifs

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Mar 15;26(6):843-4. doi: 10.1093/bioinformatics/btq026. Epub 2010 Jan 26.
iMotifs: an integrated sequence motif visualization and analysis environment.
Piipari M1, Down TA, Saini H, Enright A, Hubbard TJ.

scan-x 1.1 – Find Motifs within any Sequence data set

scan-x 1.1

:: DESCRIPTION

scan-x is a software tool designed to find motifs within any sequence data set. The first large scale scan was performed using all available human, mouse, fly and yeast phosphorylation and acetylation data to perform a scan for undiscovered modification sites.

::DEVELOPER

Schwartz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2009 Feb;8(2):365-79. doi: 10.1074/mcp.M800332-MCP200. Epub 2008 Oct 28.
Predicting protein post-translational modifications using meta-analysis of proteome scale data sets.
Schwartz D, Chou MF, Church GM.

Curr Protoc Bioinformatics. 2011 Dec;Chapter 13:Unit 13.16.. doi: 10.1002/0471250953.bi1316s36.
Using the scan-x Web site to predict protein post-translational modifications.
Chou MF, Schwartz D.

Harvest 1.1.2 – A Suite of Core-genome Alignment and Visualization tools

Harvest 1.1.2

:: DESCRIPTION

Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes. Harvest includes: Parsnp, a fast core-genome multi-aligner, Gingr, a dynamic visual platform, and harvest-tools, providing both a reference compressed binary archive and format conversion tools.

::DEVELOPER

The University of Maryland Center for Bioinformatics and Computational Biology (CBCB)

:: SCREENSHOTS

Harvest

:: REQUIREMENTS

  • Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Harvest

:: MORE INFORMATION

Citation

Treangen TJ, Ondov BD, Koren S, Phillippy AM.
Rapid Core-Genome Alignment and Visualization for Thousands of Microbial Genomes.”
bioRxiv (2014). doi: http://dx.doi.org/10.1101/007351

MetAMOS 1.5rc3 – Metagenomic Assembly pipeline for AMOS

MetAMOS 1.5rc3

:: DESCRIPTION

MetAMOS is an open source and modular metagenomic assembly and analysis pipeline. MetAMOS represents an important step towards fully automated metagenomic analysis, starting with next-generation sequencing reads and producing genomic scaffolds, open-reading frames and taxonomic or functional annotations.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

MetAMOS 

:: REQUIREMENTS

  • Linux
  • Java
  • Perl 

:: DOWNLOAD

 MetAMOS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 May 3;15:126. doi: 10.1186/1471-2105-15-126.
Automated ensemble assembly and validation of microbial genomes.
Koren S1, Treangen TJ, Hill CM, Pop M, Phillippy AM.

Genome Biol. 2013 Jan 15;14(1):R2.
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.