AGILE v1.0 – Methodologies for Genome Mining and Annotation

AGILE v1.0

:: DESCRIPTION

The goal of AGILE (Assembled Genome minIng pipeLinE) is to mine and annotate genes from a target genome using a set of reference genes from a closely related taxon.

::DEVELOPER

AGILE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

AGILE

:: MORE INFORMATION

Citation

Hughes GM, Teeling EC.
AGILE: an assembled genome mining pipeline.
Bioinformatics. 2019 Apr 1;35(7):1252-1254. doi: 10.1093/bioinformatics/bty781. PMID: 30184049.

Apollo 2.6.5 – Genome Annotation Viewer & Editor

Apollo 2.6.5

:: DESCRIPTION

Apollo is the first instantaneous, collaborative genomic annotation editor available on the Web.

Web Apollo is designed to support geographically dispersed researchers, and the work of a distributed community is coordinated through automatic synchronization: all edits in one client are instantly pushed to all other clients, allowing users to see annotation updates from collaborators in real-time during the editing process.

::DEVELOPER

Apollo team

:: SCREENSHOTS

WebApollo

:: REQUIREMENTS

  • Mac OsX / Linux /Solaris / Unix
  • Tomcat
  • Perl
  • BioPerl
  • Blat
  • JAVA

:: DOWNLOAD

Apollo

:: MORE INFORMATION

Citation:

Dunn NA, Unni DR, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE.
Apollo: Democratizing genome annotation.
PLoS Comput Biol. 2019 Feb 6;15(2):e1006790. doi: 10.1371/journal.pcbi.1006790. PMID: 30726205; PMCID: PMC6380598.

CHASM 3.0 / CHASMplus 1.0 – Cancer-specific High-throughput Annotation of Somatic Mutations

CHASM 3.0 / CHASMplus 1.0

:: DESCRIPTION

CHASM is a method that predicts the functional significance of somatic missense mutations observed in the genomes of cancer cells, allowing mutations to be prioritized in subsequent functional studies, based on the probability that they give the cells a selective survival advantage.

CHASMplus is a machine learning method that accurately distinguishes between driver and passenger missense mutations, even for those found at low frequencies or are cancer type-specific.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • MySQL Server
  • Python module MySQLdb

:: DOWNLOAD

CHASMplus

:: MORE INFORMATION

Citation

Tokheim C, Karchin R.
CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers.
Cell Syst. 2019 Jul 24;9(1):9-23.e8. doi: 10.1016/j.cels.2019.05.005. Epub 2019 Jun 12. PMID: 31202631; PMCID: PMC6857794.

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.
Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R.
Bioinformatics. 2011 Aug 1;27(15):2147-8. doi: 10.1093/bioinformatics/btr357. Epub 2011 Jun 17.

POLYVIEW-2D / POLYVIEW-3D / POLYVIEW-MM – Protein Structure Annotation using Sequence Profiles / Structures / Motions

POLYVIEW-2D / POLYVIEW-3D / POLYVIEW-MM

:: DESCRIPTION

The POLYVIEW-2D protein structure visualization server can be used to generate amino acid sequence annotations, such as secondary structure, relative solvent accessibility, evolutionary conservation, and physico-chemical property profiles. It can also be used to identify residues involved in protein-protein interactions and highlight other important sites and motifs.

POLYVIEW-3D is a web-based tool for macromolecular structure visualization and analysis. In particular, it provides a wide array of options for automated structural and functional analysis of proteins and their complexes. This tutorial aims to describe and illustrate the available rendering options and annotation capabilities of POLYVIEW-3D.

POLYVIEW-MM (Molecular Motion) enables animation of trajectories generated by Molecular Dynamics and related simulation techniques, as well as visualization of alternative conformers, e.g., obtained as a result of protein structure prediction methods or small molecule docking, using an intuitive web-based interface.

:: SCREENSHOTS

N/A

::DEVELOPER

Meller Lab

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

POLYVIEW: a flexible visualization tool for structural and functional annotations of proteins.
Porollo AA, Adamczak R, Meller J.
Bioinformatics. 2004 Oct 12;20(15):2460-2. Epub 2004 Apr 8.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W662-6. doi: 10.1093/nar/gkq445. Epub 2010 May 26.
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations.
Porollo A, Meller J.

ANNIE – Protein Sequence Annotation and Interpretation Environment

ANNIE

:: DESCRIPTION

ANNIE is a comprehensive de novo protein annotation system that integrates a large number of indispensable algorithms used in everyday sequence analytic work.

::DEVELOPER

Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W435-40. doi: 10.1093/nar/gkp254. Epub 2009 Apr 23.
ANNIE: integrated de novo protein sequence annotation.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G

GenomeRunner 4.0 – Annotation and Enrichment of Next-Gen Sequencing Data

GenomeRunner 4.0

:: DESCRIPTION

GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser.

::DEVELOPER

GenomeRunner team

:: SCREENSHOTS

GenomeRunner

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GenomeRunner

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):419-20. doi: 10.1093/bioinformatics/btr666. Epub 2011 Dec 6.
GenomeRunner: automating genome exploration.
Dozmorov MG1, Cara LR, Giles CB, Wren JD.

DDF2GO – Translate high throughput DDF Proteomics data into GO CC Annotations

DDF2GO

:: DESCRIPTION

DDF2GO uses high throughput differential detergent fractionation (DDF) proteomics data to assign experimentally based Gene Ontology (GO) cellular component (CC) annotations.

:: DEVELOPER

AgBase

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DDF2GO

:: MORE INFORMATION

Citation

“A high-throughput experiment-based method to identify subcellular localization,”
Lakshmi R Pillai, et al.

MultiGlycan 1.0 – Annotation of Glycomic Profiles in the LC-MS data

MultiGlycan 1.0

:: DESCRIPTION

MultiGlycan helps user to gather glycan profile information from LC-MS Spectra. It also reports quantity of specific glycan composition.

::DEVELOPER

Haixu Tang

:: SCREENSHOTS

MultiGlycan

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MultiGlycan

 :: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1706-7. doi: 10.1093/bioinformatics/btt190. Epub 2013 Apr 22.
Automated annotation and quantification of glycans using liquid chromatography-mass spectrometry.
Yu CY1, Mayampurath A, Hu Y, Zhou S, Mechref Y, Tang H.

CNVannotator 20131114 – Annotation Server for Copy Number Variation (CNV) in Humans

CNVannotator 20131114

:: DESCRIPTION

CNVannotator is a web server that accepts an input set of human genomic positions in a user-friendly tabular format.

::DEVELOPER

Bioinformatics and Systems Medicine Laboratory,

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2013 Nov 14;8(11):e80170. doi: 10.1371/journal.pone.0080170. eCollection 2013.
CNVannotator: a comprehensive annotation server for copy number variation in the human genome.
Zhao M1, Zhao Z.

DeepDRBP-2L – Genome Annotation predictor for identifying DNA-binding proteins and RNA-binding proteins

DeepDRBP-2L

:: DESCRIPTION

DeepDRBP-2L is a new computational predictor for identifying DBPs, RBPs and DRBPs by combining Convolutional Neural Network (CNN) and the Long Short-Term Memory (LSTM).

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Zhang J, Chen Q, Liu B.
DeepDRBP-2L: A New Genome Annotation Predictor for Identifying DNA-Binding Proteins and RNA-Binding Proteins Using Convolutional Neural Network and Long Short-Term Memory.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul-Aug;18(4):1451-1463. doi: 10.1109/TCBB.2019.2952338. Epub 2021 Aug 6. PMID: 31722485.