Sequence Manipulation Suite:
Version 2
  • The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.
  • See the about the Sequence Manipulation Suite page for more information about individual Sequence Manipulation Suite programs.
  • You can easily mirror the Sequence Manipulation Suite on your own web site, or you can use it off-line.
  • This version of the Sequence Manipulation Suite represents a complete re-write of the previous version. The new version is much faster and has many new features. The previous version of the Sequence Manipulation Suite can still be accessed.
  • Send questions and comments to

new window | home | citation
Tue Sep 20 18:12:27 2011
Valid XHTML 1.0! Valid CSS!

Perform secondary structure predictions on protein sequences.

Find binding specificity information about DNA-protein complexes.

Find information about the binding specificity of DNA-binding proteins.

Use this web-based sequence motif visualization system to display sequence motif information in its appropriate three-dimensional (3D) context.

Protein function prediction and annotation in an integrated environment powered by web service.

Use to predict function from de novo protein sequences.

Search for short active protein sequences with demonstrated biological activities.

Search for ungapped segments corresponding to the most highly conserved regions of proteins.

Identify and measure surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules.

Classify metalloproteins and some other complex bioinorganic proteins using the concept of bioinorganic motif.

Design and interpret experiments to identify protein phosphorylation sites by Edman sequencing of unseparated peptides.

To search for catalytic residue annotation for enzymes in the Protein Data Bank.

Predict protein function using Gene Ontology.

Automatically calculate evolutionary conservation scores of key amino acid residues and map them on protein structures.

Mine the protein structure space.

Predict short linear motifs (3-8 residues) in a set of protein sequences.

A web client for visualizing protein sequence feature information using DAS.

Identify the domain architecture within a protein sequence.

Predict functional sites in eukaryotic proteins.

Use a collection of tools for protein analyses.

Predict potential protein post-translational modifications and find potential single amino acid substitutions in peptides.

Search for information related to the catalytic mechanisms of enzymes.

An integrated feature-based function prediction server for vertebrate proteomes.

Identify the closest matching PRINTS sequence motif fingerprints in a protein sequence.

Search for functional annotation of important sites in proteins with known structures.

Produce 3D conformations of small drug compounds.

A database presenting experiment-based results in human proteomics.

Conduct exhaustive intermediate profile searches of a set of homologous protein sequences.

Design protein mutations in site-directed mutagenesis.

Annotate protein using this integrated annotation resource.

Identify protein family (and DNA) domains, patterns, motifs, protein families, and functional sites.

Conduct comprehensive protein function annotation.

Interactive forecasting of protein interaction hot spots.

Identify protein kinase-specific phosphorylation sites based on sequences and coupling patterns.

Database containing pairs of structural analogs and their alignments.

Find sequence patterns in DNA and protein sequences.

Identify phylogenetic motifs in protein sequences.

A web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases.

A web service for analyze and annotate mass spectrometry data.

Find information about alpha-helical transmembrane proteins.

Find structural segments or motifs for protein structures.

Visualize protein sequence motifs on the 3D protein structures.

Find presence of any known protein motif (Prosite and Pfam) in a protein sequence.

Recognize spatial chemical binding patterns common to a set of protein structures.

Analyze proteins for the presence of N-terminal N-myristoylation site.

Find the presence of N-Glycosylation sites in human proteins.

Find the presence of O-GalNAc (mucin type) glycosylation sites in mammalian proteins.

Analyze eukaryotic proteins for the presence of serine, threonine and tyrosine phosphorylation sites.

Find possible kinase specific phosphorylation sites in eukaryotic proteins.

Predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences.

Find information about patented nucleotide and protein sequences.

Search for information about glycoproteins with O-linked and C-linked glycosylation sites.

Find information about protein sequence annotations.

A server to predict protein active site residues.

Search for structural and functional information on the protein functional sites.

Search 3D protein fragments similar in structure to known active, binding and posttranslational modification sites.

Conduct genome wide functional and structural analysis.

Search for phosphorylation data of any protein of interest.

Search for information on prokaryotic proteins that undergo serine, threonine, or tyrosine phosphorylation.

Determine correct names for proteins.

Web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.

Find homologous protein-protein interactions across multiple species.

Search your query sequence against PROSITE pattern database for protein motifs.

Find information about protein-RNA complexes from the Protein Data Bank (PDB).

Search for comprehensive sequence, structural, functional and bibliographic information on metalloproteins and other complex proteins, with an emphasis on active site structure and function.

Identify protein families and domains for a given protein sequence.

A comprehensive database of pattern-recognition receptors and their ligands.

Search for short nucleotide or peptide sequences such as cis-elements in nucleotide sequences or small domains and motifs in protein sequences.

Database specialized in documenting human PPBD-containing proteins and PPBD-mediated interactions.

Predicts potential protease cleavage sites and sites cleaved by chemicals in a given protein sequence.

Predict combined transmembrane topology and signal peptides.

Search for eukaryotic phosphorylation sites.

Search for 3D structure and functional annotation of phosphorylation sites in proteins.

Search the database of in vivo phosphorylation sites of human and mouse proteins

Find information about polyglutamine (polyQ) repeats.

Find the presence of protein motifs and patterns in an amino acid sequence.

Predict signal peptide sequences and their cleavage positions in bacterial and eukaryotic amino acid sequences.

Predict lipid posttranslational modifications and localization signals from protein sequences.

Predict protein functions based on known structures.

Predict the location of potential protein-protein binding sites for unbound proteins.

Identify short linear signatures in protein termini.

Analyze and identify newly obtained protein sequences.

Predict protein binding sites in a protein sequence based on geometrical analysis of protein tertiary substructures.

Search for evolutionarily conserved motif-like patterns in protein sequences.

A web-based server for prediction of RNA-binding sites in proteins.

Web-based server for analyzing and predicting RNA binding sites in proteins.

Search for similarities between proteins by simultaneous matching of multiple motifs.

Predict residues in protein sequences that determine the proteins' functional specificity.

Predict specificity-determining residues in protein families.

Find shared motifs in proteins with a common attribute.

Predict recombination sites from amino acid sequence.

Conduct in silico sumoylation sites prediction.

Compare annotated protein surface regions and find putative surface functional sites.

Search for motifs and patterns within protein sequences.

Search for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains.

Find information about populations carrying polymorphisms within protein binding pockets that make them susceptible to serious adverse drug reaction (SADR).

Search the presence of a motif in either amino acid sequence or nucleotide sequence.

Detect subfamily specific positions from a multiple alignment.

Search for known ligand binding sites of proteins within the PDB.

A graph-based approach for the detection and identification of repetitive elements in low-complexity sequences.

Predict the presence of tyrosine sulfation sites in protein sequences

Look at protein structure from a ligand and binding site perspective.

Use a collection of bioinformatics tools at this portal site.

Find information about tandem repeats in proteins that carry fundamental biological functions and are related to a number of human diseases.

Find information about functional residues in alpha-helical and beta-barrel membrane proteins.

Database of domains and motifs with conservative location in transmembrane proteins.

Search for highly conserved and specific protein sequence motifs.

Predict functional sites in protein sequence alignments use different methodologies.

Find de novo protein motifs from chromatin immunoprecipitation data.

Scan query structures for functional sites in both proteins and nucleic acids.

Analyze quantitative structure-activity relationship of related protein families.

Search for ungapped alignments of highly conserved regions among a protein family or superfamily.

An expert system for predicting ligand-binding residues in protein structures.

Automatically identify spatially interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage.

Predict functionally important regions in proteins of known structure.