gffcompare 0.9.6f – Comparing, Annotating, Merging and Tracking Transcripts in GFF files

gffcompare 0.9.6f

:: DESCRIPTION

gffcompare is a program for comparing, annotating, merging and tracking transcripts in GFF(General Feature Format) files

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 gffcompare

:: MORE INFORMATION

MuD – Annotating the Affect of Missense Mutations on the Protein’s Function

MuD

:: DESCRIPTION

MuD (Mutation Detector) is a server for annotating the affect of missense mutations on the protein’s function using sequence and structural features

::DEVELOPER

The Ben-Tal Lab of Computational Structural Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W523-8. doi: 10.1093/nar/gkq528. Epub 2010 Jun 11.
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data.
Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N.

MitoAnnotator – Annotating Fish Mitogenomic Sequence

MitoAnnotator

:: DESCRIPTION

MitoFish is a comprehensive and standardized fish mitochondrial genome database.

MitoAnnotator is a pipeline for annotating fish mitogenomic sequence fully automatically and accurately just in five minutes.

::DEVELOPER

Atmosphere and Ocean Research Institute, the University of Tokyo,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Biol Evol. 2013 Nov;30(11):2531-40. doi: 10.1093/molbev/mst141. Epub 2013 Aug 16.
MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.
Iwasaki W1, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, Nishida M.

DANN – Annotating Pathogenicity of Genetic Variants

DANN

:: DESCRIPTION

DANN is a deep learning approach for annotating the pathogenicity of genetic variants.

::DEVELOPER

CBCL Lab (Computational Biology and Computational Learning) @ UCI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Python

:: DOWNLOAD

 DANN

:: MORE INFORMATION

Citation

DANN: a deep learning approach for annotating the pathogenicity of genetic variants.
Quang D, Chen Y, Xie X.
Bioinformatics. 2015 Mar 1;31(5):761-3. doi: 10.1093/bioinformatics/btu703.

SNiPA v2 – a tool for Annotating and Browsing Genetic Variants

SNiPA v2

:: DESCRIPTION

SNiPA offers both functional annotations and linkage disequilibrium information for bi-allelic genomic variants (SNPs and SNVs). SNiPA combines LD data based on the 1000 Genomes Project with various annotation layers, such as gene annotations, phenotypic trait associations, and expression-/metabolic quantitative trait loci.

::DEVELOPER

SNiPA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SNiPA: an interactive, genetic variant-centered annotation browser.
Arnold M, Raffler J, Pfeufer A, Suhre K, Kastenmüller G.
Bioinformatics. 2014 Nov 26. pii: btu779

AGPS – Annotating Genes with Positive Samples

AGPS

:: DESCRIPTION

AGPS is a software for defining negative samples in gene function prediction.

::DEVELOPER

ChenLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • MatLab

:: DOWNLOAD

 AGPS

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Jan 28;9:57. doi: 10.1186/1471-2105-9-57.
Gene function prediction using labeled and unlabeled data.
Zhao XM1, Wang Y, Chen L, Aihara K.

trieFinder – Annotating Digital Gene Expression (DGE) Tags

trieFinder

:: DESCRIPTION

The trieFinder program is designed to rapidly map Digital Gene Expression (DGE) tags of various lengths to RefSeq, UniGene, and/or genomic sequences. It annotates the tags with information from the sequence files, providing output in a format that is amenable to both transcript quantification and the detection of novel transcripts.

::DEVELOPER

trieFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • Perl

:: DOWNLOAD

  trieFinder

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Oct 13;15:329. doi: 10.1186/1471-2105-15-329.
trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.
Renaud G, LaFave MC, Liang J, Wolfsberg TG, Burgess SM

GeneNomenclatureUtils – Tools for Annotating Genes and Comparing Gene Lists with Community Resources

GeneNomenclatureUtils

:: DESCRIPTION

GeneNomenclatureUtils is a command-line utilities for using MGI, Entrez, HGNC, PubMed, and OMIM files.

::DEVELOPER

Genes to Cognition (G2C)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GeneNomenclatureUtils

:: MORE INFORMATION

PathBuilder 1.0 – open source Software for Annotating and Developing Pathway Resources

PathBuilder 1.0

:: DESCRIPTION

PathBuilder is an open source software to annotate biological information pertaining to signaling pathways and, with minimal additional effort, to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events via manual or automatic methods.

::DEVELOPER

The Pandey LabInstitute of Bioinformatics , India

:: SCREENSHOTS

PathBuilder

:: REQUIREMENTS

  • Linux / MacOsX /Windows
  • Zope
  • MySQL
  • Python

:: DOWNLOAD

   PathBuilder

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Nov 1;25(21):2860-2. doi: 10.1093/bioinformatics/btp453.
PathBuilder–open source software for annotating and developing pathway resources.
Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad TS, Ramachandra YL, Mohan S, Pandey A.

MAXIT 8.120 – An application for Processing and Annotating of Macromolecular Structure data

MAXIT 8.120

:: DESCRIPTION

The Maxit Program Suite was developed by the PDB (Protein Data Bank) and NDB (Nucleic Acid Database) to assist in the processing and curation of macromolecular structure data.

::DEVELOPER

RCSB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  MAXIT, Source Code

:: MORE INFORMATION