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Each entry contains referenced information about the RNA, including sequences, structural information, genomic context, expression, subcellular localization, conservation, functional evidence and other relevant information. lncRNAdb can be searched by querying published RNA names and aliases, sequences, species and associated protein-coding ...
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.
Separate modules extend Biopython's capabilities to sequence alignment, protein structure, population genetics, phylogenetics, sequence motifs, and machine learning. Biopython is one of a number of Bio* projects designed to reduce code duplication in computational biology. [6]
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 ...
The four search types phmmer, hmmsearch, hmmscan and jackhmmer are supported (see Programs). The search function accepts single sequences as well as sequence alignments or profile HMMs. [10] The search results are accompanied by a report on the taxonomic breakdown, and the domain organisation of the hits. Search results can then be filtered ...
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 starts by predicting the expected mutation probabilities for each position. For a certain residue, a sequence window of ten total surrounding residues is selected as seen in the image. Then, Biegert and Söding compared the sequence window to a library with thousands of context profiles.
The development of protein domain databases such as Pfam (Protein Families Database) [10] allow us to find known domains within a query sequence, providing evidence for likely functions. The dcGO website [ 11 ] contains annotations to both the individual domains and supra-domains (i.e., combinations of two or more successive domains), thus via ...