Utility includes some mini popular bioinformatics analysis tools written in javascript or applet. If you know some other applications which are pretty useful, please give us some advice at your free time.

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Bioverse

       BioverseViewerV2(applet)     An enhanced Java graph applet interface for visualizing interactomes of Bioverse interaction database

GlycanBuilder

       GlycanBuilder(applet)     A fast, intuitive and flexible software tool for building and displaying glycan structures

Vimida

       Vimida(applet)     A Java-applet for Visualization of Microarray Data using linear and non-linear principal components analysis (PCA)

Sequence Manipulation Suite

       Sequence Analysis

             codon_plot(js)     Plots codon frequency (according to the codon table you enter) for each codon in a DNA sequence.

             codon_usage(js)     Returns a standard codon usage table.

             cpg_islands(js)     Returns a list of potential CpG islands.

             dna_pattern(js)     Returns positions of the patterns you enter.

             dna_stats(js)     Returns basic sequence statistics.

             fuzzy_search_dna(js)     Returns sequences that are identical or similar to a query sequence.

             fuzzy_search_protein(js)     Returns sequences that are identical or similar to a query sequence.

             ident_sim(js)     Accepts aligned sequences in FASTA format and calculates the identity and similarity of each sequence pair.

             multi_rev_trans(js)     Can be used to predict a DNA sequence in another species using a protein sequence alignment.

             mutate_for_digest(js)     Finds DNA sequences that can easily be converted to a restriction site.

             orf_find(js)     Determines the positions of open reading frames.

             pairwise_align_codons(js)     Returns the optimal global alignment for two coding DNA sequences.

             pairwise_align_dna(js)     Returns the optimal global alignment for two DNA sequences.

             pairwise_align_protein(js)     Returns the optimal global alignment for two protein sequences.

             pcr_primer_stats(js)     Returns a report describing PCR primer properties.

             pcr_products(js)     Generates PCR products from a template and two primer sequences.

             protein_gravy(js)     Returns the grand average of hydropathy value of protein sequences.

             protein_iep(js)     Returns the predicted isoelectric point of protein sequences.

             protein_mw(js)     Calculates the molecular weight of the protein you enter.

             protein_pattern(js)     Returns positions of the patterns you enter.

             protein_stats(js)     Returns basic sequence statistics.

             rest_digest(js)     Converts the sequence you enter into restriction fragments.

             rest_summary(js)     Returns the number and positions of restriction sites.

             rev_trans(js)     Can be used to convert protein into DNA.

             translate(js)     Returns the translation in the reading frame you specify.

       Sequence Figures

             color_align_cons(js)     Colors a sequence alignment based on sequence conservation.

             color_align_prop(js)     Colors a protein alignment based on biochemical properties of residues.

             group_dna(js)     Numbers and groups DNA according to your specifications.

             group_protein(js)     Numbers and groups amino acids according to your specifications.

             primer_map(js)     Shows PCR primer annealing sites, translations, and restriction sites.

             rest_map(js)     Shows restriction sites and protein translations.

             trans_map(js)     Shows protein translations.

       Format Conversion

             combine_fasta(js)     Combines multiple FASTA entries into a single sequence.

             embl_fasta(js)     Returns the entire sequence contained in an EMBL file in FASTA format.

             embl_feat(js)     Parses the feature table of an EMBL file and returns the feature sequences.

             embl_trans(js)     Parses the feature table of an EMBL file and returns the protein translations.

             filter_dna(js)     Filter DNA removes non-DNA characters from text.

             filter_protein(js)     Filter Protein removes non-protein characters from text.

             genbank_fasta(js)     Returns the entire sequence contained in a GenBank file in FASTA format.

             genbank_feat(js)     Parses the feature table of a GenBank file and returns the feature sequences.

             genbank_trans(js)     Parses the feature table of a GenBank file and returns the protein translations.

             one_to_three(js)     Converts single letter amino acid codes to three letter codes.

             range_extract_dna(js)     Reads a list of positions and ranges and returns those parts of a DNA sequence.

             range_extract_protein(js)     Reads a list of positions and ranges and returns those parts of a protein sequence.

             rev_comp(js)     Determines the reverse-complement, reverse, or complement of the sequence you enter.

             split_fasta(js)     Divides FASTA entries into smaller sequences.

             three_to_one(js)     Converts three letter amino acid codes to one letter codes.

       Miscellaneous

             genetic_code(js)     The genetic codes used in the Sequence Manipulation Suite.

             iupac(js)     IUPAC codes for DNA and protein.

       Random Sequences

             mutate_dna(js)     Introduces random mutations into DNA sequences.

             mutate_protein(js)     Introduces random mutations into protein sequences.

             random_coding_dna(js)     Generates a random coding sequence of the length you specify.

             random_dna(js)     Generates a random DNA sequence of the length you specify.

             random_dna_regions(js)     Replaces regions of the DNA sequences you enter with random bases.

             random_protein(js)     Generates a random protein sequence of the length you specify.

             random_protein_regions(js)     Replaces regions of the protein sequences you enter with random residues.

             sample_dna(js)     Samples bases from a DNA sequence with replacement.

             sample_protein(js)     Samples residues from a protein sequence with replacement.

             shuffle_dna(js)     Randomly shuffles the DNA sequences you enter.

             shuffle_protein(js)     Randomly shuffles the protein sequences you enter.

jalview

       jalview(applet)     Jalview is a multiple alignment editor written in Java.

WebMol

       webmol(applet)     WebMol was designed to display and analyze structural information contained in the Protein Data Bank (PDB).

References:

• http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl
• Stothard P (2000) The Sequence Manipulation Suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28:1102-1104.
• http://bioinfo-out.curie.fr/projects/vimida/
• Chang AN, McDermott J, Samudrala R. (2005), An enhanced java graph applet interface for visualizing interactomes, Bioinformatics. 21: 1741-1742.
• Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor, Bioinformatics, 20, 426-7
• Alessio C., Anne D. and Stuart M. H. (2007), The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures, Source Code for Biology and Medicine. 2:3.