Tag: Annotation

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

PhyloGena 1.04 – Automated Interactive Phylogenetic Annotation Tool

PhyloGena 1.04

:: DESCRIPTION

PhyloGena is a software tool to facilitate phylogenetic annotation of unknown sequences. It has a user-friendly graphical interface and you will intuitively learn how to use it. You can import 1, 10, 100, 1000? (see below) DNA or protein sequences and the program will search for similar sequences, construct a multiple alignment and subsequently a phylogenetic tree for all of them and show them to you. You can easily manipulate the data sets, add or remove sequences, change parameters etc. This is of great help in identifying the function and phylogenetic affiliation of ORFs and makes annotation of genes or ESTs easier and less error-prone.

::DEVELOPER

PhyloGena Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

PhyloGena

:: MORE INFORMATION

Citation:

Hanekamp K, Bohnebeck U, Beszteri B, Valentin K.
PhyloGena–a user-friendly system for automated phylogenetic annotation of unknown sequences.
Bioinformatics. 2007 Apr 1;23(7):793-801. Epub 2007 Mar 1.

Artemis v18.0.3 – Genome Browser and Annotation Tool

Artemis v18.0.3

:: DESCRIPTION

Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

Artemis

:: MORE INFORMATION

Citation

Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B
Artemis: sequence visualization and annotation.
Bioinformatics (Oxford, England) 2000;16;10;944-5

SQANTI 1.2 – Structural and Quality Annotation of Novel Transcript Isoforms

SQANTI 1.2

:: DESCRIPTION

SQANTI is a pipeline for the in-depth characterization of isoforms obtained by full-length transcript sequencing, which are commonly returned in a fasta file format without any extra information about gene/transcript annotation or attribute description. SQANTI provides a wide range of descriptors of transcript quality and generates a graphical report to aid in the interpretation of the sequencing results.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • Perl
  • R package

:: DOWNLOAD

 SQANTI

:: MORE INFORMATION

Citation

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.
Genome Res. 2018 Feb 9. doi: 10.1101/gr.222976.117. [Epub ahead of print] Erratum in: Genome Res. 2018 Jul;28(7):1096.
PMID: 29440222