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 Lab

:: 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.

AnnoGen 0.0.1 – Annotating Genome-wide Pragmatic features

AnnoGen 0.0.1

:: DESCRIPTION

AnnoGen is capable of annotating the proprietary pragmatic features for variable user-interested genomic regions and optionally comparing two parallel sets of genomic regions.

::DEVELOPER

Quanhu Sheng

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

AnnoGen

:: MORE INFORMATION

Citation

Sheng Q, Yu H, Oyebamiji O, Wang J, Chen D, Ness S, Zhao YY, Guo Y.
AnnoGen: annotating genome-wide pragmatic features.
Bioinformatics. 2020 May 1;36(9):2899-2901. doi: 10.1093/bioinformatics/btaa027. PMID: 31930398; PMCID: PMC7203733.

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

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.

SNiPA v3.4 – a tool for Annotating and Browsing Genetic Variants

SNiPA v3.4

:: 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

gffcompare v0.12.2 – Comparing, Annotating, Merging and Tracking Transcripts in GFF files

gffcompare v0.12.2

:: 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

Citation

Pertea G, Pertea M.
GFF Utilities: GffRead and GffCompare.
F1000Res. 2020 Apr 28;9:ISCB Comm J-304. doi: 10.12688/f1000research.23297.2. PMID: 32489650; PMCID: PMC7222033.

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.

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

Snpdat – A Simple High Throughput Analysis Tool for Annotating SNPs

Snpdat

:: DESCRIPTION

SNPdat (SNP Data Analysis Tool) is a high throughput analysis tool that can provide a comprehensive annotation of both novel and known single nucleotide polymorphisms (SNPs). It is specifically designed for use with organisms which are either not supported by other tools or have a small number of annotated SNPs available, however it can also be used to analyse datasets from organisms which are densely sampled for SNPs. It can be used for analysis of any organism with a draft sequence and annotation. SNPdat makes possible analyses involving non-model organisms that are not supported by the vast majority of SNP annotation tools currently available.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

SNPdat

:: MORE INFORMATION

Citation

BMC Bioinformatics, 14, 45 2013 Feb 8
Snpdat: Easy and Rapid Annotation of Results From De Novo Snp Discovery Projects for Model and Non-Model Organisms
Anthony G Doran , Christopher J Creevey

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.