CLC Main Workbench utilizes two algorithms for finding the alignments.This alignment algorithm has three parameters for calculating the gap costs.

Image source: QIAGEN CLC Main Workbench Sequence AlignmentД¬LC Main Workbench is efficient in aligning the nucleotides and proteins by using the Progressive alignment algorithms. Given below is a biomolecule structure generated from PDB 2R9R. A file with information on 3D Coordinates only can be used to generate entire structures. The вЂњ Generate BiomoleculeвЂќ option lets you generate biomolecules structures in CLC Main Workbench.The Protein structures can be aligned too.The transfer of annotation between the sequence and structure is feasible too. They link the sequence alignments to the molecule structure. There are some tools present in the 3D viewer that helps in linking the sequence and the structure.You can BLAST search the structure file against the PDB database.The visualization settings include- hydrogens, fog, clipping plane, 3D projection, coloring, etc. The visualization can be customized with different colors and styles of representation. You can view the protein structure in 3D.It allows the importing of molecule structure files from the Protein Data Bank (PDB) or its file in the system. FindВ function to search within a sequence.Annotation type and layouts, restriction sites, motifs, the coloring of residues.Sequence label-В adding details such as name, accession, common name, etc.The position of sequences-В shows the position of residue in a protein/DNA sequence.Double-stranded-В applies only to the double-stranded DNA sequence.Wrap sequences-В no wrap, automatic wrap, fixed wrap.Spacing-В no spacing, every 10 residues, every 3 residues frame 1, every 3 residues frame 2, every 3 residues frame 3.There are several choices in Sequence Layout. You can zoom in, zoom out, and edit the sequence.On double-clicking the sequence in the navigation area, the sequence of amino acid or DNA or RNA will appear on the view panel. This feature offers to view the sequence. The various tools and features of CLC Main Workbench are mentioned below: Sequence Editing and Viewing CLC Main Workbench is a complete and all-rounder package for thorough analysis.

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