> > Alignment Editing and Visualization

Alignment Editing and Visualization

Tools for viewing, coloring, and editing sequence alignments.

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Found 23 links

Displaying 15 links

@TOME-2Tool Content

http://abcis.cbs.cnrs.fr/AT2/

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Comparison
Sequence Comparison > Alignment Editing and Visualization

@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model building and evaluation are possible with @TOME-2 for inputted protein sequences.

NAR Web Server Issue 2009
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tagsligands molecular models phosphoprotein phosphatases protein folding protein kinases protein sequence analysis protein structural homology transcription factors

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

BoxShadeTool Content

http://www.ch.embnet.org/software/BOX_form.html

DNA > DNA and Genomic Analysis
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

Printing and shading of multiple alignment files.

This content is being maintained by lfalquet.

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tagseurope protein databases protein sequence analysis sequence alignment

CHAOS/DIALIGN WWW serverTool Content

http://dialign.gobics.de/chaos-dialign-submission

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments

The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.

NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagsalgorithms animals chickens computational biology dna sequence analysis genome genomics humans leukemia mice neoplasm dna neoplasm genes nucleic acid regulatory sequences rats sensitivity and specificity sequence alignment software validation stem cells tetraodontiformes zebrafish

EMBL-EBI FrameworkTool Content

http://www.ebi.ac.uk/Tools/sss

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.

NAR Web Server Issue 2010
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tagscomputational biology nucleic acid databases protein databases sequence alignment sequence analysis

EMBOSSTool Content

http://emboss.bioinformatics.nl/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Presentation and Format
Protein > Sequence Features
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.

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tagsmolecular biology sequence alignment

enoLOGOSTool Content

http://biodev.hgen.pitt.edu/enologos/

Sequence Comparison > Alignment Editing and Visualization

enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.

NAR Web Server Issue 2005
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tagsamino acids binding sites dna sequence analysis dna-binding proteins sequence alignment zinc fingers

EnteriXTool Content

http://enterix.cbcb.umd.edu/

Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella sequence alignment

ESPriptTool Content

http://espript.ibcp.fr/ESPript/ESPript/index.php

Sequence Comparison > Alignment Editing and Visualization

Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology dna-binding proteins molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

GeneDocTool Content

http://www.psc.edu/biomed/genedoc/

Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

Multiple sequence alignment editor, analyser and shading utility for Windows.

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JOYTool Content

http://tardis.nibio.go.jp/cgi-bin/joy/joy.cgi

Protein > 3-D Structure Retrieval/Viewing
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

JOY is a program for displaying 3D structural information in a multiple sequence alignment.

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tagsamino acid sequence hydrogen bonding molecular sequence data protein conformation proteins secondary protein structure sequence alignment

Kalign, Kalignvu, and MumsaTool Content

http://msa.cgb.ki.se/cgi-bin/msa.cgi

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes. Mumsa is a tool for automatic assessment of alignment quality.

NAR Web Server Issue 2006
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tagsalgorithms dna sequence analysis genome genomics nucleic acid databases protein databases protein sequence analysis reproducibility of results roc curve sequence alignment

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

NAR Web Server Issue 2006
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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

SeaviewTool Content

http://pbil.univ-lyon1.fr/software/seaview.html

Sequence Comparison > Alignment Editing and Visualization

SeaView is a graphical multiple sequence alignment editor that is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.

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tagsanimals base sequence dna molecular evolution molecular sequence data phylogeny proteins ribosomal rna sequence alignment

SequenceJuxtaposerTool Content

http://www.cs.ubc.ca/~tmm/papers/sj/

Sequence Comparison > Alignment Editing and Visualization

SequenceJuxtaposer is a tool for visualizing and comparing biomolecular sequences. Uses a visualization technique called accordion drawing that allows users to zoom into regions of interest in alignments.

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Tags associated with subcategory 'Sequence Comparison/Alignment Editing and Visualization'

sequence alignment dna sequence analysis protein sequence analysis computational biology algorithms protein databases humans animals molecular sequence data genomics software design x-ray crystallography species specificity sequence analysis theoretical models tetraodontiformes dna-binding proteins software validation proteasome endopeptidase complex stem cells zinc fingers salmonella typhi shigella flexneri bacterial genome bacterial dna rats neoplasm dna neoplasm genes conserved sequence enterobacteriaceae hydrogen bonding salmonella typhimurium genetic recombination gene rearrangement escherichia coli escherichia coli o157 consensus sequence secondary protein structure gene expression regulation dna binding sites rna sequence analysis sensitivity and specificity genetic transcription nucleic acid databases viral genome transcription factors systems integration nucleic acid regulatory sequences simian virus 40 reproducibility of results proteins evaluation studies as topic mice computer simulation genetic databases base sequence factual databases fibronectins protein conformation protein-serine-threonine kinases phylogeny messenger rna genes genetic models nucleic acid sequence homology zebrafish complementary dna protein structural homology protein kinases phosphoprotein phosphatases protein folding chickens leukemia computer systems database management systems cluster analysis chlamydophila pneumoniae ribosomal rna roc curve capripoxvirus canada amino acids cysteine endopeptidases bacterial chromosomes base composition europe ligands multienzyme complexes amino acid motifs protein biosynthesis biological models genetic code amino acid sequence amino acid sequence homology molecular biology documentation fuzzy logic salmonella molecular models nucleotidyltransferases