Tag: Annotation

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.

RCAS 1.18.0 – RNA Centric Annotation System

RCAS 1.18.0

:: DESCRIPTION

RCAS facilitates biological discovery from target regions located by methods such as Clip-Seq. RCAS automatically provides dynamic annotations for custom input files that contain transcriptomic target regions.

::DEVELOPER

Bioinformatics & Omics Data Science platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

RCAS

:: MORE INFORMATION

Citation

Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A.
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Nucleic Acids Res. 2017 Jun 2;45(10):e91. doi: 10.1093/nar/gkx120. PMID: 28334930; PMCID: PMC5449606.

dbCAN2 – Automated CAZyme Annotation

dbCAN2

:: DESCRIPTION

dbCAN2 meta server is a web server for automated Carbohydrate-active enzyme ANnotation.

::DEVELOPER

YIN LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y.
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation.
Nucleic Acids Res. 2018 Jul 2;46(W1):W95-W101. doi: 10.1093/nar/gky418. PMID: 29771380; PMCID: PMC6031026.

eCAMI – Simultaneous Classification and Motif Identification for enzyme/CAZyme annotation

eCAMI

:: DESCRIPTION

eCAMI is a Python package: (i) has the best performance in terms of accuracy and memory use for CAZyme and enzyme EC classification and annotation; (ii) the k-mer-based tools (including PPR-Hotpep, CUPP and eCAMI) perform better than homology-based tools and deep-learning tools in enzyme EC prediction.

::DEVELOPER

YIN LAB @ UNL & ZHANG LAB @ NKU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

eCAMI

:: MORE INFORMATION

Citation

Xu J, Zhang H, Zheng J, Dovoedo P, Yin Y.
eCAMI: simultaneous classification and motif identification for enzyme annotation.
Bioinformatics. 2020 Apr 1;36(7):2068-2075. doi: 10.1093/bioinformatics/btz908. PMID: 31794006.

BioSAVE 0.11 – Biological Sequence Annotation Viewer

BioSAVE 0.11

:: DESCRIPTION

BioSAVE is a program for visualising DNA or protein sequences and annotations thereof. Annotations is used in a very broad sense here, encompassing any annotation that may be expressed in GFF format.

::DEVELOPER

Richard Pollock and Boris Adryan

:: SCREENSHOTS

BioSAVE

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 BioSAVE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Mar 20;9:157. doi: 10.1186/1471-2105-9-157.
BioSAVE: display of scored annotation within a sequence context.
Pollock RF1, Adryan B.

SNPsnap – Identification and Annotation of matched SNPs

SNPsnap

:: DESCRIPTION

The SNPsnap webserver enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations.

::DEVELOPER

SNPsnap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

SNPsnap: a web-based tool for identification and annotation of matched SNPs.
Pers TH, Timshel P, Hirschhorn JN.
Bioinformatics. 2014 Oct 13. pii: btu655.

ShortStack 3.8.5 – Comprehensive Annotation and Quantification of small RNA genes

ShortStack 3.8.5

:: DESCRIPTION

ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.

::DEVELOPER

Axtell Lab @ Penn State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ShortStack

:: MORE INFORMATION

Citation:

Axtell MJ.
ShortStack: comprehensive annotation and quantification of small RNA genes.
RNA. 2013 Jun;19(6):740-51. doi: 10.1261/rna.035279.112. Epub 2013 Apr 22. PMID: 23610128; PMCID: PMC3683909.

SemanticSBML 2.0 – Annotation Checking& Merging of Systems Biology Models

SemanticSBML 2.0

:: DESCRIPTION

SemanticSBML create, check, annotate, merge SBML (System Biology Markup Lanugage) models. The program includes a graphical user interface as well as a console interface that can process batch jobs.

Semantic annotations can be used to define – among other things – the biochemical meaning of model elements. The tool semanticSBML is made to handle such annotations. It helps you to edit them and to check and merge your models.

::DEVELOPER

semanticSBML team at Humboldt University Berlin

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

SemanticSBML

:: MORE INFORMATION

Citation

For citing semanticSBML, please refer to: Krause F, Uhlendorf J., Lubitz T., Schulz M., Klipp E., Liebermeister W. (2010),
Annotation and merging of SBML models with semanticSBML,
Bioinformatics 26 (3), 421-422, doi:10.1093/bioinformatics/btp642.

YGAP – Yeast Genome Annotation Pipeline

YGAP

:: DESCRIPTION

YGAP is an online tool to annotate yeast species based on sequence and synteny conservation.

::DEVELOPER

the Wolfe Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 17;13:237. doi: 10.1186/1471-2105-13-237.
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.
Proux-Wéra E1, Armisén D, Byrne KP, Wolfe KH.

Exit mobile version