Bioinformatics Links Directory : Presentation and FormatYou 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.BoxShade- (Found June 24, 2008 ) Printing and shading of multiple alignment files.http://www.ch.embnet.org/software/BOX_form.html WAViS- (Found June 24, 2008 ) The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.http://wavis.img.cas.cz/ VisCoSe- (Found June 24, 2008 ) 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.http://viscose.ifg.uni-muenster.de/ T-COFFEE- (Found June 24, 2008 ) 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 that is more accurate than ClustalW for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. PROTOGENE turns amino acid alignments into CDS nucleotide alignments. M-Coffee is a meta-method for computing multiple sequence...http://www.tcoffee.org/ ReadSeq- (Found June 24, 2008 ) Sequence format conversion; includes GenBank, EMBL, GCG, FASTA, ASN.1, Phylip and others.http://searchlauncher.bcm.tmc.edu/seq-util/readseq.html RbDe- (Found June 24, 2008 ) 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.http://icb.med.cornell.edu/crt/RbDe/index.xml POV-Ray- (Found June 24, 2008 ) Persistence of Vision Raytracer; use in conjunction with Swiss-PdbViewer to create graphics for presentation and publication.http://www.povray.org/ LogoBar- (Found June 24, 2008 ) 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.http://www.biosci.ki.se/groups/tbu/logobar/ JOY- (Found June 24, 2008 ) JOY is a program for displaying 3D structural information in a multiple sequence alignment.http://www-cryst.bioc.cam.ac.uk/~joy/ GeneDoc- (Found June 24, 2008 ) Multiple sequence alignment editor, analyser and shading utility for Windows.http://www.psc.edu/biomed/genedoc/ |