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ICAtools [18] - original (ancient) DNA clustering package with many algorithms useful for artifact discovery or EST clustering Skipredudant EMBOSS tool [ 19 ] to remove redundant sequences from a set CLUSS Algorithm [ 20 ] to identify groups of structurally, functionally, or evolutionarily related hard-to-align protein sequences.
Software suite to search and cluster huge sequence sets. Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster: Protein: Steinegger M, Mirdita M, Galiez C, Söding J [10] 2017 USEARCH Ultra-fast sequence analysis tool: Both: Edgar, R. C. (2010). "Search and clustering orders of magnitude faster than BLAST". Bioinformatics.
Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some specific sense defined by the analyst) to each other than to those in other groups (clusters).
MNHN-Tree-Tools is an opensource phylogenetics inference software working on nucleic and protein sequences. Clustering of DNA or protein sequences and phylogenetic tree inference from a set of sequences. At the core it employs a distance-density based approach. Thomas Haschka, Loïc Ponger, Christophe Escudé and Julien Mozziconacci [28 ...
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences.
The water molecules are interacting with the protein and tend to cluster at the protein's polar regions. This led to the idea of immersing the purified protein crystal in other solvents (e.g. ethanol, isopropanol, etc.) to determine where these molecules cluster on the protein.
Particularly, clustering helps to analyze unstructured and high-dimensional data in the form of sequences, expressions, texts, images, and so on. Clustering is also used to gain insights into biological processes at the genomic level, e.g. gene functions, cellular processes, subtypes of cells, gene regulation, and metabolic processes. [26]
Cluster analysis has placed a group of down regulated genes in the upper left corner. In the field of molecular biology, gene expression profiling is the measurement of the activity (the expression) of thousands of genes at once, to create a global picture of cellular function. These profiles can, for example, distinguish between cells that are ...