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Showing 20 records out of 38 total
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Categories: proteomics, (protein sequences and identification, mass spectrometry and 2-DE data) - Software type(s): website - tool
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.
Categories: proteomics, (protein characterisation and function) - Software type(s): website - tool
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.
Categories: proteomics, (post-translational modification) - Software type(s): website - tool
The ChloroP server predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website, CLI, GUI - tool
Multiple alignment of nucleic acid and protein sequences.
Categories: proteomics, (protein characterisation and function) - Software type(s): website - tool
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
Categories: proteomics, (protein sequences and identification, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Redundancy reduction in a set of aligned or unaligned sequences
Categories: proteomics - Software type(s): website - database/tool
Set of bioinformatics tools, databases and courses
Categories: genomics - Software type(s): CLI - tool
Tagger and fetchGWI are tools which allow searching short sequence tags against entire genomes or mRNA reference sequence databases.
Categories: proteomics, (mass spectrometry and 2-DE data, protein characterisation and function, post-translational modification) - Software type(s): website - tool
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.
Categories: proteomics, (post-translational modification) - Software type(s): website - tool
Calculate the mass of an oligosaccharide structure.
Categories: proteomics, (protein sequences and identification, mass spectrometry and 2-DE data, post-translational modification) - Software type(s): website - tool
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.
Categories: protein sequences and identification, genomics - Software type(s): website - tool
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
Categories: proteomics, (protein sequences and identification, protein characterisation and function, families, patterns and profiles) - Software type(s): website - database/tool
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.
Categories: proteomics, (families, patterns and profiles) - Software type(s): website - tool
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.
Categories: proteomics, (post-translational modification), genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website, GUI - tool
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.
Categories: proteomics, (protein sequences and identification, similarity search/alignment), genomics, (sequence alignment, similarity search) - Software type(s): website, CLI - tool
LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally.
Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
C++ program for HMM models
Categories: proteomics, (protein structure), structural bioinformatics - Software type(s): website, CLI - tool
predicting coiled-coils in protein sequences
Categories: genomics, (characterisation/annotation), phylogeny/evolution - Software type(s): website - database
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.
Categories: proteomics, (families, patterns and profiles, similarity search/alignment) - Software type(s): website - database/tool
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.
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