Tag: Multiple Sequence Alignment

Multi-Relief – Recognize Specificity Determining Residues from Multiple Sequence Alignment

Multi-Relief

:: DESCRIPTION

multi-RELIEF is a novel approach for identifying specificity residues that is based on RELIEF, a state-of-the-art Machine-Learning technique for feature weighting.

::DEVELOPER

Elena Marchiori

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • MatLab

:: DOWNLOAD

 Multi-Relief

:: MORE INFORMATION

Citation

K. Ye, A. Feenstra, A.Ijzerman, J. Heringa, E. Marchiori.
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine Learning approach for feature weighting.
Bioinformatics, 24(1), pp. 18-25, 2008.

Sequlator 2013 – Free Multiple Sequence Alignment Editor

Sequlator 2013

:: DESCRIPTION

Sequlator is a free multiple sequence alignment editor with a pairwise alignment function. Sequlator can be used merely as a tool for viewing and manipulating multiple alignments of nucleotide sequences, but the main purpose of Sequlator is to facilitate analysis of sequences produced by sequencing of newly isolated recombinant plasmids or PCR fragments. During molecular cloning of gene transcripts or DNA fragments undesired spontaneous mutations may be introduced into recombinant vectors.

::DEVELOPER

sequlator@gmail.com.

:: SCREENSHOTS

Sequlator

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java 

:: DOWNLOAD

 Sequlator

:: MORE INFORMATION

REFINER 200911 – Refinement of Multiple Sequence Alignments

REFINER 200911

:: DESCRIPTION

REFINER is an algorithm that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core model of a protein family.

::DEVELOPER

Computational Biophysics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 REFINER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Nov 14;7:499.
State of the art: refinement of multiple sequence alignments.
Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA, Bryant SH.

Mulan – Multiple Sequence Alignment tool

Mulan

:: DESCRIPTION

Mulan performs local multiple DNA sequence alignments of finished and draft-quality sequences.It identifies transcription factor binding sites evolutionarily conserved across multiple species.

::DEVELOPER

Ivan Ovcharenko Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mulan: multiple-sequence alignment to predict functional elements in genomic sequences.
Loots GG, Ovcharenko I.
Methods Mol Biol. 2007;395:237-54.

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.
Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.
Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.

SuiteMSA 1.3.22B – Visual tools for the comparison and analysis of Multiple Sequence Alignments

SuiteMSA 1.3.22B

:: DESCRIPTION

SuiteMSA is a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent) or disagree (are inconsistent).

::DEVELOPER

Catherine Lee Anderson

:: SCREENSHOTS

SuiteMSA

::REQUIREMENTS

  • MacOsX/Linux/Windows
  • Java

:: DOWNLOAD

 SuiteMSA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 May 21;12:184. doi: 10.1186/1471-2105-12-184.
SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation.
Anderson CL, Strope CL, Moriyama EN.

JProfileGrid 2.0.5 – Multiple Sequence Alignment tool that generates ProfileGrids

JProfileGrid 2.0.5

:: DESCRIPTION

JProfileGrid is a Java-based multiple sequence alignment tool that generates ProfileGrids for analysis and export. ProfileGrids are a new paradigm for visualizing and analyzing MSAs in a concise representation. For a protein sequence, a ProfileGrid matrix contains positional amino acid counts highlighted according to the frequency of the characters in the alignment. ProfileGrids facilitate comparative nanoanatomy analysis of macromolecules.

::DEVELOPER

JProfileGrid Team

:: SCREENSHOTS

JProfileGrid

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Java

:: DOWNLOAD

 JProfileGrid

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2008 Dec 22;9:554. doi: 10.1186/1471-2105-9-554.
ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family.
Roca AI, Almada AE, Abajian AC.

PCMA – Profile Consistency Multiple sequence Alignment

PCMA

:: DESCRIPTION

PCMA constructs a multiple sequence alignment given a set of protein sequences.

::DEVELOPER

Grishin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PCMA

:: MORE INFORMATION

Citation:

J.Pei, R.I.Sadreyev, and N.V.Grishin (2003)
“PCMA: Fast and Accurate Multiple Sequence Alignment Based on Profile Consistency“.
Bioinformatics 19(3): 427-428.

PCPMer 3.5.6 – Determine Conserved Regions in multiple Sequence Alignments

PCPMer 3.5.6

:: DESCRIPTION

PCPMer (Physical Chemical Property Based Motif Analyzer ) is a software package for determining conserved regions in multiple sequence alignments. The software represents each of the 20 naturally occuring amino acids by five quantitative descriptors and can detect motifs (short regions of significant conservation) in aligned sequences based on relative entropy or physicochemical similarity. It can be then used to search for related proteins in a protein sequence database and map the variability data on a 3D structure (to make a stereophysicochemical variability plot, or SVP). Such plots are particularly useful for identifying the spatial relationships of highly conserved or variable residues to one another.

::DEVELOPER

 PCPMer Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PCPMer

:: MORE INFORMATION

Citation:

Schein, C.H., Zhou, B. and Braun, W.
Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses.
Virol. J. Apr 21;2(1):40, 2005

 

PFAAT 2.0 – Multiple Sequence Alignments Analysis

PFAAT 2.0

:: DESCRIPTION

PFAAT (Protein Family Alignment Annotation Tool)is a Java application that allows one to edit, analyze, and annotate multiple sequence alignments. The annotation features are a key component as they provide a framework to for further sequence, structure and statistical analysis.

::DEVELOPER

Neogenesis Drug Discovery

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac OsX/Linux
  • java 

:: DOWNLOAD

  PFAAT

:: MORE INFORMATION

Citation:

Daniel R Caffrey et al.
PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments
BMC Bioinformatics 2007, 8:381

MultAlin 5.4.1 – Multiple Sequence Alignment

MultAlin 5.4.1

:: DESCRIPTION

multalinis software that will allow you to align simultaneously several biological sequences

::DEVELOPER

Florence Corpet

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MultAlin

:: MORE INFORMATION

Citation

“Multiple sequence alignment with hierarchical clustering”
F. CORPET, 1988,
Nucl. Acids Res., 16 (22), 10881-10890