BioAnnote 2.0.0 – Annotate Biomedical Texts by using different high-quality online Resources

BioAnnote 2.0.0

:: DESCRIPTION

BioAnnote is a desktop application is able to annotate biomedical texts by using different high-quality online resources, such as Medlineplus and Freebase.

::DEVELOPER

SING Group.

:: SCREENSHOTS

BioAnnote

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • java

:: DOWNLOAD

 BioAnnote

:: MORE INFORMATION

Citation

Comput Methods Programs Biomed. 2013 Jul;111(1):139-47. doi: 10.1016/j.cmpb.2013.03.007.
BioAnnote: a software platform for annotating biomedical documents with application in medical learning environments.
López-Fernández H, Reboiro-Jato M, Glez-Peña D, Aparicio F, Gachet D, Buenaga M, Fdez-Riverola F.

CEGMA 2.5 – Annotate Core Genes in Eukaryotic Genomes

CEGMA 2.5

:: DESCRIPTION

CEGMA (Core Eukaryotic Genes Mapping Approach) is a software for building a highly reliable set of gene annotations in the absence of experimental data.

:DEVELOPER

Korf Lab at the University of California, Davis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CEGMA

:: MORE INFORMATION

Citation

Genis Parra, Keith Bradnam and Ian Korf.
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Bioinformatics, 23: 1061-1067 (2007)

Kelviz v3.3.1 – Plot and Annotate Genetic data analysis results

Kelviz v3.3.1

:: DESCRIPTION

Kelviz is a graphing application designed to plot and annotate genetic data analysis results for easy review and publication. It is designed for use with Kelvin analysis results, but can make use of any data file that follows roughly the same conventions.

::DEVELOPER

Battelle Center for Mathematical Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

 Kelviz

:: MORE INFORMATION

Citation

Valentine-Cooper, J., et al. ”
Kelviz: A Graphing Tool For Statistical Evidence In Human Genetics.
Poster presented at: Road to Collaboration. NCH and OSU Human Genetics Community Symposium; 2014 May 20; Columbus, OH

TASR 1.1 – Annotate Transposable Elements using siRNAs Mapping

TASR 1.1

:: DESCRIPTION

TASR (Transposon Annotation using Small RNAs) is a bioinformatic pipeline that can annotate Transposable elements using siRNAs mapping

::DEVELOPER

TASR team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 TASR

:: MORE INFORMATION

Citation

A new approach for annotation of transposable elements using small RNA mapping.
El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA.
Nucleic Acids Res. 2015 Jul 27;43(13):e84. doi: 10.1093/nar/gkv257.

Marky 2.3.0 – Annotate Biomedical Texts using different Annotation Classes

Marky 2.3.0

:: DESCRIPTION

Marky is able to annotate biomedical texts using different annotation classes. You only need a server with php technology and one database to annotate documents with a browser. Users can enter biomedical documents to be annotated by other users and get annotations for relevant terms, such as diseases, symptoms and treatments. Whith Marky you can annote from simple documents (without any formatting) to HTML documents. So that documents can have embedded images and all power of HTML.

::DEVELOPER

SING Group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Apache
  • PHP
  • MySQL 

:: DOWNLOAD

 Marky

:: MORE INFORMATION

Citation

Comput Methods Programs Biomed. 2015 Feb;118(2):242-51. doi: 10.1016/j.cmpb.2014.11.005. Epub 2014 Nov 25.
Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects.
Pérez-Pérez M, Glez-Peña D, Fdez-Riverola F, Lourenço A.

Prokka 1.14.5 – Annotate Bacterial Draft Genome

Prokka 1.14.5

:: DESCRIPTION

Prokka is a software tool for the rapid annotation of prokaryotic genomes.

::DEVELOPER

Torsten Seemann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl
  • BioPerl
  • BLAST+
  • HMMer
  • Aragorn
  • Prodigal
  • tbl2asn
  • GNU Parallel

:: DOWNLOAD

 Prokka

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 4. [Epub ahead of print]
Prokka: rapid prokaryotic genome annotation.
Seemann T.

QuasR 1.32.0 – Quantify and Annotate Short Reads in R

QuasR 1.32.0

:: DESCRIPTION

QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification.

::DEVELOPER

Anita Lerch, Dimos Gaiditzis and Michael Stadler <michael.stadler at fmi.ch>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 QuasR

:: MORE INFORMATION

Citaton

QuasR: Quantification and annotation of short reads in R.
Gaidatzis D, Lerch A, Hahne F, Stadler MB.
Bioinformatics. 2014 Nov 21. pii: btu781.

AS-EAST 1.1.3 – Annotate and Analyzes users’ uploaded Transcript data

AS-EAST 1.1.3

:: DESCRIPTION

AS-EAST (Alternative Splicing Effects ASsessment Tools) is an online tool for the functional annotation of putative proteins encoded by transcripts generated by alternative splicing (AS).

::DEVELOPER

Nagahama Institute of Bio-Science and Technology

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 1;28(15):2076-7. doi: 10.1093/bioinformatics/bts320.
AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts.
Shionyu M, Takahashi K, Go M.

AnnoLnc 2.1 – Annotate human lncRNAs

AnnoLnc 2.1

:: DESCRIPTION

AnnoLnc2 is a web server to provide on-the-fly analysis for novel human or mouse lncRNAs.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

AnnoLnc

:: MORE INFORMATION

Citation

Ke L, Yang DC, Wang Y, Ding Y, Gao G.
AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse.
Nucleic Acids Res. 2020 Jul 2;48(W1):W230-W238. doi: 10.1093/nar/gkaa368. PMID: 32406920; PMCID: PMC7319567.

ChIPpeakAnno 3.24.2 – Annotate ChIP-seq and ChIP-chip data

ChIPpeakAnno 3.24.21

:: DESCRIPTION

ChIPpeakAnno is a Bioconductor package within the statistical programming environment R to facilitate batch annotation of enriched peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression (CAGE) or any experiments resulting in a large number of enriched genomic regions.

::DEVELOPER

Program in Gene Function and Expression@umassmed

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

  ChIPpeakAnno

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 May 11;11:237. doi: 10.1186/1471-2105-11-237.
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.
Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR.

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