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With BAR 3.0 and a sequence you can annotate when possible: function (Gene Ontology), structure (Protein Data Bank), protein domains (Pfam). Also if your sequence falls into a cluster with a structural/some structural template/s we provide an alignment towards the template/templates based on the Cluster-HMM (HMM profile) that allows you to ...
If such a template protein is found, the structure of the protein of interest can be predicted based on a pairwise sequence alignment of the query with the template protein sequence. For example, a search through the PDB database of proteins with solved 3D structure takes a few minutes.
The Chou–Fasman method predicts helices and strands in a similar fashion, first searching linearly through the sequence for a "nucleation" region of high helix or strand probability and then extending the region until a subsequent four-residue window carries a probability of less than 1.
A profile HMM modelling a multiple sequence alignment. HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. [2] Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments.
Casanovo is a machine learning model that uses a transformer neural network architecture to translate the sequence of peaks in a tandem mass spectrum into the sequence of amino acids that comprise the generating peptide, enabling de novo peptide sequencing without prior information. [34] InstaNovo Open source
CS-BLAST improves further upon this concept. The figure illustrates the sequence to sequence and profile to sequence equivalence with the alignment matrix. The query profile results from the artificial mutations in which the bar heights are proportional to the corresponding amino acid probabilities.
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UTOPIA (User-friendly Tools for Operating Informatics Applications) is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains applications for viewing and aligning protein sequences, rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects.