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.

 

ChIPseeker 1.22.0 – ChIP peak Annotation, Comparison & Visualization

ChIPseeker 1.22.0

:: DESCRIPTION

ChIPseeker is an R package for annotating ChIP-seq data analysis.

::DEVELOPER

Guangchuang YU,

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/MacOsX
  • R
  • Bioconductor

:: DOWNLOAD

 ChIPseeker

:: MORE INFORMATION

Citation:

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.
Yu G, Wang LG, He QY.
Bioinformatics. 2015 Mar 11. pii: btv145.

VARIFI – Variant Identification, Filtering and Annotation of Amplicon Sequencing Data

VARIFI

:: DESCRIPTION

VARIFI is a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)).

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data.
Krunic M, Venhuizen P, Müllauer L, Kaserer B, von Haeseler A.
J Pers Med. 2019 Feb 1;9(1). pii: E10. doi: 10.3390/jpm9010010.

Mason – JavaScript Widget for Viewing Sequence Features and Annotations

Mason

:: DESCRIPTION

Mason is a JavaScript and SVG-based viewer meant to display annotated regions or features of DNA and protein sequences.

::DEVELOPER

Mason team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JavaScript

:: DOWNLOAD

 Mason

:: MORE INFORMATION

Citation

BMC Res Notes. 2015 Dec;8(1):1009. doi: 10.1186/s13104-015-1009-z. Epub 2015 Mar 7.
Mason: a JavaScript web site widget for visualizing and comparing annotated features in nucleotide or protein sequences.
Jaschob D1, Davis TN, Riffle M.

snpEff 4.3T – Variant Annotation and Effect Prediction Tool

snpEff 4.3T

:: DESCRIPTION

snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

SnpSift is a collection of tools to manipulate VCF (variant call format) files.

SnpEffWrapper takes a VCF and applies Annotations from a GFF using SnpEff

::DEVELOPER

snpEff team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

snpEff / SnpEffWrapper

:: MORE INFORMATION

Citation

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.
Fly (Austin). 2012 Apr-Jun;6(2):80-92.

Companion – Easy and reliable Parasite Genome Annotation

Companion

:: DESCRIPTION

Companion is a web server providing parasite genome annotation as a service using a reference-based approach.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C et al.
Companion: a web server for annotation and analysis of parasite genomes.
Nucleic Acids Res. 2016 Jul 8;44(W1):W29-34. doi: 10.1093/nar/gkw292. Epub 2016 Apr 21.

MetaTISA – Translation Initiation Site Annotation for Metagenomes

MetaTISA

:: DESCRIPTION

MetaTISA is tool with an aim to improve translationa initiation sites (TISs) prediction of current gene-finders for metagenomes. The method employs a two-step strategy to predict TISs by first clustering metagenomic fragments into phylogenetic groups and then predicting TISs independently for each group in an unsupervised manner. As evaluated on experimentally verified TISs, MetaTISA greatly improves the accuracies of TIS prediction of current gene-finders.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 MetaTISA

:: MORE INFORMATION

Citation

Gang-Qing Hu, Jiang-Tao Guo, Yong-Chu Liu, and Huaiqiu Zhu.
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.
Bioinformatics 2009,25(14):1843-1845.

Pegasus 0.3.1 – Fusion Annotation and Prediction

Pegasus 0.3.1

:: DESCRIPTION

Pegasus annotates biologically functional gene fusion candidates. Pegasus provides a common interface for various gene fusion detection tools, annotation of reading frame events, reconstruction of novel fusion proteins, annotation of preserved functional domains (e.g. kinases).

::DEVELOPER

EDA (Electronic Design Automation Group)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

  Pegasus

:: MORE INFORMATION

Citation

Abate F., Zairis S., Ficarra E., Acquaviva A., Wiggins C.H., Frattini V., Lasorella A., Iavarone A., Inghirami G., Rabadan R.,
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
BMC SYSTEMS BIOLOGY vol. 8 n. 97, 2014. DOI: 10.1186/s12918-014-0097-z

APAT 1.4.1 – Automated Protein Annotation Tool

APAT 1.4.1

:: DESCRIPTION

APAT ,Automated Protein Annotation Tool. We have determined that the output can be described using one of 6 forms of data: numeric or textual annotation of residues, domains (residue ranges) or whole sequences. A tool may produce a combination of such outputs. With this in mind, an XML data-type definition (DTD) was designed to store the output of any server (`Automated Protein Annotation Tool Markup Language’, APATML).

APAT lets you write simple wrappers for annotation servers which then generate APATML as output. Our display program will then format that as HTML (including colouring of residues and graphs) for you to view, or you may write your own programs to extract and analyze the data.

::DEVELOPER

Andrew C.R. Martin’s Bioinformatics Group at UCL

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 APAT

:: MORE INFORMATION

Citation

S. Vishnu V. Deevi Andrew C. R. Martin
An extensible automated protein annotation tool: standardizing input and output using validated XML
Bioinformatics, 22,291-296.

ProSAT+ – Protein Structure Annotation Tool

ProSAT+

:: DESCRIPTION

ProSAT+ (PRO: tein S: tructure A: nnotation T: ool-plus) is a tool to explore the relation between sequence and structural properties.

::DEVELOPER

Heidelberg Institute for Theoretical Studies

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ProSAT+: visualizing sequence annotations on 3D structure.
Stank A, Richter S, Wade RC.
Protein Eng Des Sel. 2016 Jun 9. pii: gzw021