MotifNet – Web-server for Network Motif analysis

MotifNet

:: DESCRIPTION

MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes.

::DEVELOPER

Yeger-Lotem Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Smoly IY, Lerman E, Ziv-Ukelson M, Yeger-Lotem E.
MotifNet: a web-server for network motif analysis.
Bioinformatics. 2017 Jun 15;33(12):1907-1909. doi: 10.1093/bioinformatics/btx056. PMID: 28165111.

FFLtool – Web Server for TF-miRNA-target Feed Forward Loop analysis

FFLtool

:: DESCRIPTION

FFLtool is a webserver for analyzing Feed Forward Loop (FFL) regulatory motifs among transcription factors (TFs), microRNAs (miRNAs) and genes.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Xie GY, Xia M, Miao YR, Luo M, Zhang Q, Guo AY.
FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human.
Bioinformatics. 2020 Apr 15;36(8):2605-2607. doi: 10.1093/bioinformatics/btz929. PMID: 31830251.

CLIP-Explorer – Web Server for CLIP-Seq data analysis

CLIP-Explorer

:: DESCRIPTION

Galaxy CLIP-Explorer is a webserver to process, analyse and visualise CLIP-Seq data.

::DEVELOPER

the Freiburg Galaxy Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Heyl F, Maticzka D, Uhl M, Backofen R.
Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.
Gigascience. 2020 Nov 11;9(11):giaa108. doi: 10.1093/gigascience/giaa108. PMID: 33179042; PMCID: PMC7657819.

repRNA – Web Server for Generating Various Modes of RNA Sequences

repRNA

:: DESCRIPTION

repRNA (representations of RNA sequences) is a web server for generating various modes of RNA sequences

::DEVELOPER

Bin Liu’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Genet Genomics. 2015 Jun 18.
repRNA: a web server for generating various feature vectors of RNA sequences.
Liu B1, Liu F, Fang L, Wang X, Chou KC.

WebMGA – Web Server for fast Metagenomic Sequence Analysis

WebMGA

:: DESCRIPTION

WebMGA is a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc.

::DEVELOPER

Group of Weizhong Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

  No

:: MORE INFORMATION

Citation:

BMC Genomics. 2011 Sep 7;12:444. doi: 10.1186/1471-2164-12-444.
WebMGA: a customizable web server for fast metagenomic sequence analysis.
Wu S1, Zhu Z, Fu L, Niu B, Li W.

PROSPER – Protease Substrate Specificity Webserver

PROSPER

 

:: DESCRIPTION

PROSPER (PROtease substrate SPecificity servER) is an integrated feature-based webserver for in silico prediction of protease substrates and their cleavage sites for twenty-four different protease types, covering four major protease families- Aspartic (A), Cysteine (C), Metallo (M) and Serine (S).

::DEVELOPER

Whisstock Laboratory,  Monash University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Web Server
  • Perl

:: DOWNLOAD

 PROSPER

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(11):e50300. doi: 10.1371/journal.pone.0050300.
PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.
Song J, Tan H, Perry AJ, Akutsu T, Webb GI, Whisstock JC, Pike RN.

XenoSite – Metabolism Prediction Web Server

XenoSite

:: DESCRIPTION

XenoSite Web provides prediction web services for small molecule biochemistry. XenoSite Web can be used by medicinal chemists and biologists to make predictions about the human in vivo metabolism of small molecules.

::DEVELOPER

S Joshua Swamidass

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

XenoSite-Server: A Web-Available Site of Metabolism Prediction Tool.
Matlock MK, Hughes TB, Swamidass SJ.
Bioinformatics. 2014 Nov 18. pii: btu761.

DARIO / plantDARIO – Web Server for the analysis of (Plant) Short RNAs

DARIO / plantDARIO

:: DESCRIPTION

DARIO is a free web server for the analysis of short RNAs from high throughput sequencing data.

plantDARIO is a free web server for the analysis of plant small non-coding RNAs from small RNA-Seq data.

::DEVELOPER

the Hoffmann Junior Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W112-7. doi: 10.1093/nar/gkr357. Epub 2011 May 27.
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.
Fasold M1, Langenberger D, Binder H, Stadler PF, Hoffmann S.

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.
Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF.
Front Plant Sci. 2014 Dec 23;5:708. doi: 10.3389/fpls.2014.00708. eCollection 2014.

MicroGen – Web Server for Microarray Experiments

MicroGen

:: DESCRIPTION

MicroGen is MIAME compliant web-based information system for managing all the information completely characterizing spotted microarray experiments and the produced data. Based on experiment workflow, it supports distributed collaborative work in the production pipeline of spotted microarray experiments.

::DEVELOPER

Masseroli Marco, Ph.D

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows
  • Access
  • Excel

:: DOWNLOAD

  MicroGen

:: MORE INFORMATION

Citation

Burgarella S, Cattaneo D, Pinciroli F, Masseroli M.
MicroGen: a MIAME compliant Web system for microarray experiment information and workflow management.
BMC Bioinformatics 2005 Dec. 1; 6(Suppl 4): S6, p.1-6.

PredictFold-PSS-3D1D – Protein Fold Recognition Web Server

PredictFold-PSS-3D1D

:: DESCRIPTION

The PredictFold PSS-3D1D is a fold recognition server based on Protein Secondary Structure and 3D1D Profiles.

::DEVELOPER

Research Group of Dr.S.Parthasarathy

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Ganesan K & Parthasarathy S (2013)
PredictFold-PSS-3D1D: A Protein Fold Recognition Server for Predicting Folds from the Twilight Zone Sequences.
Current Bioinformatics. 8(5):552-556.

J Struct Funct Genomics. 2011 Dec;12(4):181-9. doi: 10.1007/s10969-011-9119-x. Epub 2011 Dec 3.
PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences.
Ganesan K1, Parthasarathy S.

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