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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 ...
PredictProtein (PP) is an automatic service that searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. Users send a protein sequence and receive a single file with results from database comparisons and prediction methods.
A graph-based algorithm that constructs a graph of the sequence. no [11] SubSeqer: 2008 web: A graph-based approach for the detection and identification of repetitive elements in low–complexity sequences. no [12] ANNIE: 2009 web: This method creates an automation of the sequence analytic process. no [13] LPS-annotate 2011 on request
sequence - Overall generic and amyloidogenic regions based on the consensus PASTA 2.0 [30] 2014 Web Server - PASTA 2.0: Secondary structure-related. Predicts the most aggregation-prone portions and the corresponding β-strand inter-molecular pairing for multiple input sequences. sequence top pairings and energies, mutations and protein-protein
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
MegAlign Pro (Lasergene Molecular Biology) Software to align DNA, RNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including MUSCLE, Mauve, MAFFT, Clustal Omega, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis. Both: Both: DNASTAR: 1993-2016 MUMmer suffix ...
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
Similarly, Light-Attention uses machine learning methods to predict ten different common subcellular locations. [ 12 ] The first model to generalize protein subcellular localization to all cell line does so by leveraging images of subcellular landmark stains (i.e., nuclear, plasma membrane, and endoplasmic reticulum markers) across multiple ...