UVWORD – Comparison of DNA Sequences

UVWORD

:: DESCRIPTION

UVWORD determines the number of times that each DNA word present in a sequence (target) is found in a second sequence (source), a procedure that we have called oligonucleotide profiling.

::DEVELOPER

Bioinformatics Unit, Instituto de Biomedicina de Valencia (CSIC) / Universidad de Valencia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux

:: DOWNLOAD

UVWORD

:: MORE INFORMATION

Citation

BMC Res Notes. 2008 Feb 28;1:5. doi: 10.1186/1756-0500-1-5.
Fast comparison of DNA sequences by oligonucleotide profiling.
Arnau V1, Gallach M, Marín I.

RCARE – RNA-Seq Comparison and Annotation of RNA Editing

RCARE

:: DESCRIPTION

RCARE searches, annotates and visualizes RNA editing sites using previously known thousands of editing sites.

RCARE conversion utilities is a set of python-based utilities which convert FASTQ and BAM(binary format for storing sequence data) into VCF(variant call format) and compare RNA to DNA VCF files which are derived from the same sample.

::DEVELOPER

SNUBI (Snubi’s Not Unics, Biomedical Informatics.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

RCARE conversion utilities

:: MORE INFORMATION

Citation:

BMC Med Genomics. 2015 May 29;8 Suppl 2:S8. doi: 10.1186/1755-8794-8-S2-S8.
RCARE: RNA Sequence Comparison and Annotation for RNA Editing.
Lee S, Joung JG, Park C, Park J, Kim JH.

RSmatch 2.0 – Comparison of RNA structures

RSmatch 2.0

:: DESCRIPTION

RSmatch is a package for comparing RNA structures via 1) pair-wise and DB searches; 2) multiple structure alignment with common structure computation; 3)iterative DB searches.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

RSmatch

Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA.
RADAR: a web server for RNA data analysis and research.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W300-4. doi: 10.1093/nar/gkm253. Epub 2007 May 21. PMID: 17517784; PMCID: PMC1933136.

BEACON – Automated tool for Bacterial gEnome Annotation ComparisON

BEACON

:: DESCRIPTION

BEACON is a software tool that compares annotations of a particular genome from different Annotation Methods (AMs). It uses GenBank format as input and derives Extended Annotation (EA) along side listing original annotations from individual AMs.

::DEVELOPER

BEACON team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Web server

:: DOWNLOAD

BEACON

:: MORE INFORMATION

Citation

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.
Kalkatawi M, Alam I, Bajic VB.
BMC Genomics. 2015 Aug 18;16(1):616. doi: 10.1186/s12864-015-1826-4.

Easyfig 2.2.5 – Genome Comparison Visualizer

Easyfig 2.2.5

:: DESCRIPTION

Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).

::DEVELOPER

Beatson Microbial Genomics Lab.

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Python

:: DOWNLOAD

Easyfig

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 1;27(7):1009-10. doi: 10.1093/bioinformatics/btr039. Epub 2011 Jan 28.
Easyfig: a genome comparison visualizer.
Sullivan MJ1, Petty NK, Beatson SA.

SeqVISTA 1.81 – Sequence Feature Visualization & Comparison

SeqVISTA 1.81

:: DESCRIPTION

SeqVISTA presents a holistic, graphical view of features annotated on nucleotide or protein sequences. This interactive tool highlights the residues in the sequence that correspond to features chosen by the user, and allows easy searching for sequence motifs or extraction of particular subsequences. SeqVISTA is able to display results from diverse sequence analysis tools in an integrated fashion, and aims to provide much-needed unity to the bioinformatics resources scattered around the Internet. SeqVISTA may be launched on a GenBank record by a single click of a button installed in the web browser.

::DEVELOPER

Zlab

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux / Mac OsX
JAVA

:: DOWNLOAD

SeqVISTA

:: MORE INFORMATION

Citation:

Zhenjun Hu1 , Martin Frith , Tianhua Niu and Zhiping Weng ; “SeqVISTA: A Graphical Tool for Sequence Feature Visualization and Comparison” ; BMC Bioinformatics 2003, 4:1doi:10.1186/1471-2105-4-1

ClusCo 0.3 – Clustering and Comparison of Protein Models

ClusCo 0.3

:: DESCRIPTION

ClusCo is a software for GPU/CPU clustering and comparison of protein models.

::DEVELOPER

Laboratory of Theory of Biopolymers, University of Warsaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ClusCo

:: MORE INFORMATION

Citation

ClusCo: clustering and comparison of protein models.
Jamroz M, Kolinski A.
BMC Bioinformatics. 2013 Feb 22;14:62. doi: 10.1186/1471-2105-14-62.

SMAP 2.0 – Software for Ligand Binding Site Comparison

SMAP 2.0

:: DESCRIPTION

SMAP software package is designed for the comparison and the similarity search of protein three-dimensional motifs independent on the sequence order.

::DEVELOPER

Lei Xie

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows
Perl

:: DOWNLOAD

SMAP

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W441-4. doi: 10.1093/nar/gkq400. Epub 2010 May 19.
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.
Ren J1, Xie L, Li WW, Bourne PE.

EvoPPI 1.0 – Inter-specific comparisons from PPI Databases

EvoPPI 1.0

:: DESCRIPTION

EvoPPI allows the easy comparison of publicly available data from the main Protein-Protein Interaction (PPI) databases for distinct species.

::DEVELOPER

SING Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

EvoPPI

:: MORE INFORMATION

Citation

Vázquez N, Rocha S, López-Fernández H, Torres A, Camacho R, Fdez-Riverola F, Vieira J, Vieira CP, Reboiro-Jato M.
EvoPPI 1.0: a Web Platform for Within- and Between-Species Multiple Interactome Comparisons and Application to Nine PolyQ Proteins Determining Neurodegenerative Diseases.
Interdiscip Sci. 2019 Mar;11(1):45-56. doi: 10.1007/s12539-019-00317-y. Epub 2019 Feb 1. PMID: 30707359.

ProPhylo 1.02 – Phylogenetic Profile comparison program using Partial Phylogenetic Profile algorithm

ProPhylo 1.02

:: DESCRIPTION

ProPhylo is a high-performance parallel software to run phylogenetic profile searches at genome-scale.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

ProPhylo

:: MORE INFORMATION

Citation

Basu, M. K., Selengut, J. D., Haft, D. H.
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
BMC Bioinformatics. 2011 Dec 01; 12: 434.