Tag: Comparison

NetConfer – Exploration and Comparisons of Biological Networks

NetConfer

:: DESCRIPTION

NetConfer is a web based tool designed for comparative analysis of multiple interaction networks. It implements various analysis methods organized as workflows.

::DEVELOPER

NetConfer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nagpal S, Baksi KD, Kuntal BK, Mande SS.
NetConfer: a web application for comparative analysis of multiple biological networks.
BMC Biol. 2020 May 19;18(1):53. doi: 10.1186/s12915-020-00781-9. Erratum in: BMC Biol. 2020 Oct 22;18(1):147. PMID: 32430035; PMCID: PMC7236966.

STOVCA 3.95 – Comparison, Ranking and Evaluation of Structure Alignments

STOVCA 3.95

:: DESCRIPTION

STOVCA (STructural OVerlap CAlculator) is a software that takes as input a pairwise structure superposition of proteins, DNA or RNA in PDB format generated by any software and produces a standardized structural alignment and its corresponding similarity measures, according to the parameters provided by the user. Therefore, STOVCA allows the direct comparison and ranking of structural superpositions generated by any structure superposition software

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX

:: DOWNLOAD

 STOVCA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):47-53. doi: 10.1093/bioinformatics/bts600. Epub 2012 Oct 11.
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments.
Slater AW1, Castellanos JI, Sippl MJ, Melo F.

CompaGB 1.4 – Genome Browsers Comparison

CompaGB 1.4

:: DESCRIPTION

CompaGB is a framework providing facilities to evaluate and compare Genome Browsers functionalities.

::DEVELOPER

CompaGB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CompaGB: An open framework for genome browsers comparison.
Lacroix T, Loux V, Gendrault A, Gibrat JF, Chiapello H.
BMC Res Notes. 2011 May 4;4:133. doi: 10.1186/1756-0500-4-133.

dali_sp – Script for DaliLite to perform Serial Structure Comparison

dali_sp

:: DESCRIPTION

dali_sp is a wrapper script for DaliLite to perform serial structure comparison and to merge output pairwise alignments into single multiple alignment.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 dali_sp

:: MORE INFORMATION

Survcomp 1.40.0 – Performance Assessment and Comparison for Survival Analysis

Survcomp 1.40.0

:: DESCRIPTION

Survcomp is an R package providing functions to assess and to compare the performance of risk prediction (survival) models.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 Survcomp

:: MORE INFORMATION

Citation:

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.
Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B.
Bioinformatics. 2011 Nov 15;27(22):3206-8. doi: 10.1093/bioinformatics/btr511.

STAMP 1.1 – Tool-kit for DNA Motif Comparison

STAMP 1.1

:: DESCRIPTION

STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input motifs against the chosen database (or alternatively against a user-provided dataset), and lists of the highest-scoring matches are returned. Such similarity-search functionality is expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs.

:: DEVELOPER

Benos Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 STAMP

:: MORE INFORMATION

Citation:

S Mahony, PV Benos,
“STAMP: a web tool for exploring DNA-binding motif similarities“,
Nucleic Acids Research (2007) 35(Web Server issue):W253-W258.

DiPhiSeq 0.2.0 – Robust Comparison of Expression levels

DiPhiSeq 0.2.0

:: DESCRIPTION

DiPhiSeq is an R package of robust tests for differential dispersion and differential expression in RNA-Sequencing Data

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/  Linux / WIndows
  • R Package

:: DOWNLOAD

DiPhiSeq

:: MORE INFORMATION

Citation

Bioinformatics, 35 (13), 2235-2242 2019 Jul 1
DiPhiSeq: Robust Comparison of Expression Levels on RNA-Seq Data With Large Sample Sizes
Jun Li , Alicia T Lamere

UnderII – Regulatory Sequences Comparison

UnderII

:: DESCRIPTION

UnderII is a software of alignment-free comparison of regulatory sequences (cis-regulatory modules).

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UnderII

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jul-Aug;11(4):628-37. doi: 10.1109/TCBB.2014.2306830.
Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison.
Comin M, Verzotto D.

RRS – Comparison of regulatory DNA Sequences

RRS

:: DESCRIPTION

RRS (Regulatory Region Scoring)  is a new computational framework for the detection of functional conservation of regulatory sequences using predicted occupancy levels of transcription factors of interest.

::DEVELOPER

Dr Sascha Ott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C /R

:: DOWNLOAD

 RRS

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Oct 1;26(19):2391-7. doi: 10.1093/bioinformatics/btq453. Epub 2010 Aug 9.
An alignment-free model for comparison of regulatory sequences.
Koohy H1, Dyer NP, Reid JE, Koentges G, Ott S.

STON – Protein 3D Structure Comparison

STON

:: DESCRIPTION

STON is a new algorithm to find aligned residues in two proteins with desired rmsd value.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Comput Biol Med. 2009 Feb;39(2):166-72. doi: 10.1016/j.compbiomed.2008.12.004. Epub 2009 Jan 23.
STON: A novel method for protein three-dimensional structure comparison.
Eslahchi C1, Pezeshk H, Sadeghi M, Massoud Rahimi A, Maboudi Afkham H, Arab S.

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