MeDuSa 1.6 – Multi-draft based Scaffolder

MeDuSa 1.6

:: DESCRIPTION

MeDuSa (Multi-Draft based Scaffolder) is a draft genome scaffolder that uses multiple reference genomes in a graph-based approach.

::DEVELOPER

Florence Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • Java

:: DOWNLOAD

  MeDuSa

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Mar 25. pii: btv171.
MeDuSa: a multi-draft based scaffolder.
Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M

PTMcode 2 – Known and predicted PTM Functional Associations

PTMcode 2

:: DESCRIPTION

PTMcode is a web resource for known and predicted functional associations between protein post-translational modifications (PTMs) within and between proteins.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Minguez P, Letunic I, Parca L, Garcia-Alonso L, Dopazo J, Huerta-Cepas J, Bork P.
Nucleic Acids Res. 2015 Jan;43(Database issue):D494-502. doi: 10.1093/nar/gku1081

NGLess 0.6.1 / NG-meta-profiler 0.9.1 – NGS Processing with Less Work

NGLess 0.6.1 / NG-meta-profiler 0.9.1

:: DESCRIPTION

NGLess is a domain-specific language for NGS (next-generation sequencing data) processing.

NG-meta-profiler is a collection of predefined pipelines for processing shotgun metagenomes.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NGLess , NG-meta-profiler

:: MORE INFORMATION

Citation

Microbiome. 2019 Jun 3;7(1):84. doi: 10.1186/s40168-019-0684-8.
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.
Coelho LP, Alves R, Monteiro P, Huerta-Cepas J, Freitas AT, Bork P

SIAMCAT 1.5.0 – Statistical Inference of Associations between Microbial Communities

SIAMCAT 1.5.0

:: DESCRIPTION

SIAMCAT is a modular framework for the statistical inference of associations between microbial communities and host phenotypes, such as disease states in clinical case-control studies. SIAMCAT is based on LASSO models, which offer distinctive advantages for model interpretation and microbial biomarker selection and avoid overfitting issues that can arise in naive combinations of feature selection and cross-validation.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • R

:: DOWNLOAD

SIAMCAT

:: MORE INFORMATION

mOTUs 2.5.1 – Tool for Marker Gene-based OTU (mOTU) Profiling

mOTUs 2.5.1

:: DESCRIPTION

The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

mOTUs

:: MORE INFORMATION

Citation

Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese, et al.
Nature Communications 10, Article number: 1014 (2019): https://doi.org/10.1038/s41467-019-08844-4

eggNOG 5.0 – Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups

eggNOG 5.0

:: DESCRIPTION

eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P.
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314. doi: 10.1093/nar/gky1085.

eggNOG-mapper 2.0.1 – Fast Genome-wide Functional Annotation through Orthology Assignment

eggNOG-mapper 2.0.1

:: DESCRIPTION

eggNOG-mapper is a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

eggNOG-mapper

:: MORE INFORMATION

Citation

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering & Peer Bork.
Mol Biol Evol (2017) doi: 10.1093/molbev/msx148.

iPath 3.0 – Interactive Pathways Explorer

iPath 3.0

:: DESCRIPTION

iPath (interactive Pathways Explorer) is a web-based tool for the visualization, analysis and customization of the various pathways maps. Its primary map summarizes the metabolism in biological systems as annotated to date. Nodes in the map correspond to various chemical compounds and edges represent series of enzymatic reactions.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 iPath

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2018 Jul 2;46(W1):W510-W513. doi: 10.1093/nar/gky299.
iPath3.0: interactive pathways explorer v3.
Darzi Y, Letunic I, Bork P, Yamada T.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W412-5. Epub 2011 May 5.
iPath2.0: interactive pathway explorer.
Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P.

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.

 

SMART 8.0 – Analysis of Protein Domain Architectures

SMART 8.0

:: DESCRIPTION

SMART (Simple Modular Architecture Research Tool) is an online resource for the identification and annotation of protein domains and the analysis of protein domain architectures.More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Letunic I, Doerks T, Bork P
SMART: recent updates, new developments and status in 2015
Nucleic Acids Res 2014; doi:10.1093/nar/gku949

Letunic et al. (2012)
SMART 7: recent updates to the protein domain annotation resource
Nucleic Acids Res , doi:10.1093/nar/gkr931