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Showing 18 records out of 38 total
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Categories: proteomics, (post-translational modification) - Software type(s): website - tool
Predict N-terminal myristoylation of proteins by neural networks. Myristoylator uses ensembles of neural networks, in order to learn to discriminate positive and negative sequences for N-myristoylation.
Categories: proteomics, (protein characterisation and function) - Software type(s): website - tool
PeptideCutter predicts potential substrate cleavage sites, cleaved by proteases or chemicals in a given protein sequence. The tool returns the query sequence with the possible cleavage sites mapped on it and/or a table of cleavage site positions.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - tool
Cleave a protein sequence with a chosen enzyme/protease, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest. If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications, and can highlight peptides whose masses may be affected by database conflicts, polymorphisms or splice variants.
Categories: proteomics, (families, patterns and profiles, similarity search/alignment) - Software type(s): library - tool
The pftools are a collection of programs to build, calibrate, and search biological sequences with generalized profiles. Generalized profiles are an extension of position specific scoring matrices by including position specific scores for insertions and deletions. They correspond to a matrix representation of a multiple sequence alignment that can be used to search distant homologous sequences and precisely align sequences to the model.
Categories: genomics, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
Categories: proteomics, (families, patterns and profiles) - Software type(s): website - database
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Categories: proteomics, (protein characterisation and function) - Software type(s): website - tool
Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI (isoelectric point), amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).
Categories: proteomics, (protein characterisation and function) - Software type(s): website - tool
Compute and represent the profile produced by any amino acid scale on a selected protein sequence. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but ProtScale provides more than 50 predefined scales entered from the literature.
Categories: proteomics, (families, patterns and profiles) - Software type(s): website, CLI - tool
Scan protein sequence(s) against PROSITE, or search for hits by specific motif(s) in protein sequence database(s). ScanProsite may be used alternatively in quick scan mode or advanced scan mode.
Categories: similarity search/alignment, similarity search - Software type(s): website - tool
Sequerome is a web based Java tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for protein and nucleic acid analysis. It provides a web-based sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis.
Categories: proteomics, (similarity search/alignment) - Software type(s): website - tool
SIM finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence. Results can be viewed with LALNVIEW, a graphical viewer program for pairwise alignments.
Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
SSA is a software package for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site such as a transcription initiation site. The programs provided by this web server are the following: generation of a constraint profile (Cpr); generation of a signal list (SList); generation of a signal occurrence profile (OProf); pattern optimization tool (PatOp); find motifs around functional sites (FindM), and extract sequences around functional sites (FromFPS).
Categories: proteomics, (post-translational modification) - Software type(s): website - tool
The Sulfinator is a software tool able to predict tyrosine sulfation sites in protein sequences. It employs four different Hidden Markov Models that were built to recognise sulfated tyrosine residues located N-terminally, within sequence windows of more than 25 amino acids and C-terminally, as well as sulfated tyrosines clustered within 25 amino acid windows, respectively. All four HMMs contain the distilled information from one multiple sequence alignment.
Categories: genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website - database
SwissRegulon is a database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a clear and comprehensible graphical form.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website, CLI - tool
A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. Includes M-Coffee, R-Coffee, Expresso, PSI-Coffee, iRMSD-APDB.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - tool
Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw.
Categories: proteomics, (protein sequences and identification, protein characterisation and function, similarity search/alignment) - Software type(s): website - database
The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation).
Categories: proteomics, (protein sequences and identification, protein characterisation and function, post-translational modification, protein-protein interaction) - Software type(s): website - database
UniProtKB/Swiss-Prot is the manually annotated component of UniProtKB. It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.
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