Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.
Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques.
The ChloroP server predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.
Multiple alignment of nucleic acid and protein sequences.
Compute the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences
Redundancy reduction in a set of aligned or unaligned sequences
Set of bioinformatics tools, databases and courses
Tagger and fetchGWI are tools which allow searching short sequence tags against entire genomes or mRNA reference sequence databases.
Predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides. The experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot/TrEMBL entry or from a user-entered sequence, and mass differences are used to better characterise the protein of interest.
Calculate the mass of an oligosaccharide structure.
Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides.
, mass spectrometry (MS, MS/MS, LC-MS)
, molecular weight (MW)
, oligosaccharide (glycan, sugar)
, peptide mass fingerprinting
, post-translational modification (PTM)
, sequence analysis
, sugar epitope
Differences in codon usage preference among organisms lead to a variety of problems concerning heterologous gene expression but can be overcome by rational gene design and gene synthesis. The gcua tool displays the codon quality either in codon usage frequency values or relative adaptiveness values
HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline.
Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. Sequences that match HAMAP profiles will be annotated in the UniProtKB format by the associated annotation rules.
MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
keywords: Bayesian network
, hidden markov model (HMM)
, maximum likelihood
, next generation sequencing (NGS)
, sequence analysis
, transcription factor binding site
, transcription module
, transcription regulation
, transcription start site annotation
LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally.
C++ program for HMM models
predicting coiled-coils in protein sequences
miROrtho contains predictions of precursor miRNA genes covering many animal genomes combining evidence from sequence homology and Support Vector Machine classifiers. We provide both consistent extrapolation of already known miRBase families and novel miRNA predictions by our SVM and orthology pipeline.
Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.