Identification, 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. Protein identification mapping tools are also located here.

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eBioinformaticsResource Content

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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.

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GeneDocTool Content

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

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LogoBarTool Content

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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.

links directory index: 20
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LogoBar: bar graph visualization of protein logos with gaps200620

PICRTool Content

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The Protein Identifier Cross-Reference (PICR) service is a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm based on 100% sequence identity to proteins from over 98 distinct source databases. Mappings can be limited by source database, taxonomic ID and activity status in the source database.

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POV-RayTool Content

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

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ReadSeqTool Content

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

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The Sequence Manipulation Suite 2Tool Content

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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.

VisCoSeTool Content

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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.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
VisCoSe: visualization and comparison of consensus sequences20047

WebLogoTool Content

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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.

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