> > Presentation and Format

Presentation and Format

You can find links to several good tools for manipulating the appearance and format of protein sequences, collections of protein sequences, and alignments in this section.

RSS FeedCompact ViewList as XMLList as JSON

Found 14 links

Displaying 14 links

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.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagseurope protein databases protein sequence analysis sequence alignment

eBioinformaticsResource Content

http://www.ebioinformatics.org/

DNA > DNA and Genomic Analysis
DNA > Mapping and Assembly
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
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

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.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsmolecular biology sequence alignment

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.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

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.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsamino acid sequence hydrogen bonding molecular sequence data protein conformation proteins secondary protein structure sequence alignment

LogoBarTool Content

http://www.biosci.ki.se/groups/tbu/logobar/

Protein > Domains and Motifs
Protein > Presentation and Format
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences

LogoBar is a Java application to display protein sequence logos. With this application you can generate protein sequence logos from multiple sequence alignments that show the amino acid incidence at every position.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid motifs amino acid sequence amino acids computational biology conserved sequence molecular sequence data programming languages protein databases protein sequence analysis proteins

POV-RayTool Content

http://www.povray.org/

Protein > 3-D Structure Retrieval/Viewing
Protein > Presentation and Format

Persistence of Vision Raytracer; use in conjunction with Swiss-PdbViewer to create graphics for presentation and publication.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

RbDeTool Content

http://icb.med.cornell.edu/crt/RbDe/index.xml

Protein > 2-D Structure Prediction
Protein > Presentation and Format

Residue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.

NAR Web Server Issue 2003
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid sequence calmodulin connexins eye proteins factual databases humans membrane proteins membrane transport proteins molecular models molecular sequence data mutagenesis protein conformation protein folding proteins secondary protein structure src homology domains

ReadSeqTool Content

http://searchlauncher.bcm.tmc.edu/seq-util/readseq.html

DNA > DNA and Genomic Analysis
Protein > Presentation and Format

Sequence format conversion; includes GenBank, EMBL, GCG, FASTA, ASN.1, Phylip and others.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

The Sequence Manipulation Suite 2Tool Content

http://bioinformatics.org/sms2/

DNA > DNA and Genomic Analysis
DNA > Structure and Sequence Feature Detection
Protein > Biochemical Features
Protein > Presentation and Format
Protein > Sequence Features

The Sequence Manipulation Suite is a set of tools for tasks such as sequence format conversion, sequence presentation, analysing sequence characteristics and shuffling or generating random sequences. It can be accessed over the web, or installed locally and run through a web browser.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsdna sequence analysis protein sequence analysis

VisCoSeTool Content

http://bio.math-inf.uni-greifswald.de/viscose/

DNA > DNA and Genomic Analysis
Protein > Presentation and Format
Sequence Comparison > Analysis of Aligned Sequences

VisCoSe (Visualization and Comparison of consensus Sequences) is a web based tool that takes a set of sequences (aligned or unaligned) and calculates a consensus sequence and the conservation rates for the sequence alignment, producing an easy to interpret visualization as output. One can also compare and visualize a set of consensus sequences generated from several sequence sets.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid sequence base sequence consensus sequence database management systems molecular sequence data sequence alignment sequence analysis

WAViSTool Content

http://wavis.img.cas.cz/

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

The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsdna sequence analysis humans protein sequence analysis rna sequence analysis sequence alignment sequence analysis

WebLogoTool Content

http://weblogo.berkeley.edu/

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

WebLogo allows one to create graphical representations (sequence logos) of multiple sequence alignments. This can be done from the website and the source code for WebLogo is also available for download.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet

Tags associated with subcategory 'Protein/Presentation and Format'

sequence alignment molecular sequence data amino acid sequence protein sequence analysis proteins algorithms humans protein conformation protein databases dna sequence analysis factual databases computer simulation consensus sequence fibronectins evaluation studies as topic dna messenger rna genes rna sequence analysis sensitivity and specificity reproducibility of results protein-serine-threonine kinases genetic models phylogeny base sequence computational biology amino acids conserved sequence programming languages amino acid motifs molecular biology europe calmodulin amino acid sequence homology animals connexins eye proteins hydrogen bonding secondary protein structure database management systems sequence analysis src homology domains protein folding membrane proteins membrane transport proteins molecular models mutagenesis