Tag: Annotation

CARMO v1.0 – Comprehensive Annotation of Rice Multi-Omics

CARMO v1.0

:: DESCRIPTION

CARMO is a web-based platform providing comprehensive annotations for multi-omics data, including transcriptomic data sets, epi-genomic modification sites, SNPs from genome re-sequencing, and the large gene lists derived from these omics studies.

::DEVELOPER

Plant Bioinformatics and Functional Epigenomics Group, SIPPE, SIBS, CAS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data.
Wang J, Qi M, Liu J, Zhang Y.
Plant J. 2015 Jul;83(2):359-74. doi: 10.1111/tpj.12894.

eGATU – easy Genome Annotation Transfer Utility

eGATU

:: DESCRIPTION

eGATU (easy Genome Annotation Transfer Utility) is a light application modelled on GATU. It allows users to transfer annotations to an input genome without having to specify a reference.

::DEVELOPER

the Upton lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

eGATU

:: MORE INFORMATION

GATU – Genome Annotation Transfer Utility

GATU

:: DESCRIPTION

GATU (Genome Annotation Transfer Utility) annotates a genome based on a very closely related reference genome. The proteins/mature peptides of the reference genome are BLASTed against the genome to be annotated in order to find the genes/mature peptides in the genome to be annotated.

::DEVELOPER

the Upton lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

GATU

:: MORE INFORMATION

Citation:

Tcherepanov, T., Ehlers, A. and Upton, C. 2006.
Genome Annotation Transfer Utility (GATU): Rapid annotation of viral genomes using a closely related reference genome. BMC Genomics 7:150.

Word Add-in for Ontology – Word add-in for Annotation of Word Documents based on terms that appear in Ontologies

Word Add-in for Ontology

:: DESCRIPTION

Ontology Add-in for Word enables the annotation of Word documents based on terms that appear in Ontologies.

:: DEVELOPER

Ontology Add-in for Word team

:: SCREENSHOTS

WordOntology

:: REQUIREMENTS

  • Windows
  • Word

:: DOWNLOAD

 Word Add-in for Ontology

:: MORE INFORMATION

Citation

Fink, J. Lynn et al.
“Word add-in for ontology recognition: semantic enrichment of scientific literature.”
BMC Bioinformatics, 11.103 (2010).

BASys 1.0 – Bacterial Genome Annotation

BASys 1.0

:: DESCRIPTION

BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

BASys: a web server for automated bacterial genome annotation.
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W455-9.

ClueGO 2.0.5 – Cytoscape Plugin to Decipher Gene Ontology and Pathway Annotation Networks

ClueGO 2.0.5

:: DESCRIPTION

ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role.

::DEVELOPER

Integrative Cancer Immunology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ClueGO

:: MORE INFORMATION

Citation

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J.
Bioinformatics. 2009 Apr 15;25(8):1091-3. Epub 2009 Feb 23.

est2assembly 1.13 – Assembly and Annotation of Transcriptomes for any Species

est2assembly 1.13

:: DESCRIPTION

The est2assembly platform is the only platform for standardising transcriptome projects: go from raw trace files to an annotated GBrowse interface driven by the Seqfeature database. It accepts both Sanger and 454 sequencing technology for a denovo assembly, annotation and data mining of EST data.

::DEVELOPER

Dr Alexie Papanicolaou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 est2assembly

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Dec 24;10:447. doi: 10.1186/1471-2105-10-447.
Next generation transcriptomes for next generation genomes using est2assembly.
Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG.

RNAspace 1.2 – Platform for Non-protein-coding RNA Annotation

RNAspace 1.2

:: DESCRIPTION

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation. The platform allows running in an integrated environment a variety of ncRNA gene finders, to explore results with dedicated tools for comparison, visualization and edition of putative ncRNAs and to export them in various formats

::DEVELOPER

RNAspace Team

:: SCREENSHOTS

Document3

:: REQUIREMENTS

  • Linux
  • Python
  • cherrypy
  • cheetah
  • blastall, bl2seq
  • clustalw
  • Vienna RNA package
  • Perl

:: DOWNLOAD

 RNAspace

:: MORE INFORMATION

Citation

RNA. 2011 Nov;17(11):1947-56. doi: 10.1261/rna.2844911. Epub 2011 Sep 23.
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.
Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, Gaspin C.

ProSAT – PROtein reSidue Annotation Toolkit

ProSAT

:: DESCRIPTION

ProSAT toolkit is a set of programs that allow building SVM based models for annotating amino acid residues in protein sequences using user supplied features (like PSI-BLAST profiles, or PSIPred profiles). In particular, the toolkit builds features using a window around the residue, and is equipped with a specialized kernel function (normalized second order exponential kernel function nsoe ) along with the standard svm kernel function.

:: DEVELOPER

Professsor Huzefa Rangwala (rangwala@cs.gmu.edu) and  Professsor George Karypis

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

 ProSAT

:: MORE INFORMATION

Citation

“A kernel framework for protein residue annotation“.
Huzefa Rangwala, Christopher Kauffman and George Karypis.
Lecture Notes in Computer Science Volume 5476, 2009, pp 439-451

RAMMCAP 20130510 – Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline

RAMMCAP 20130510

:: DESCRIPTION

RAMMCAP is a metagenomic analysis package developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort.

::DEVELOPER

Group of Weizhong Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

  RAMMCAP

:: MORE INFORMATION

Citation

Weizhong Li.
Analysis and comparison of very large metagenomes with fast clustering and functional annotation.
BMC Bioinformatics 2009, 10:359 doi:10.1186/1471-2105-10-359