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AUTOASSEMBLER (Perkin Elmer) and CLUSTALX programs [ 21] were used for sequence editing and alignment purpose respectively.
A protein structure for alignment purpose is modeled as a finite, ordered sequence of three dimensional (3D) points.
Therefore, substitution matrices and gap penalties tuned to a particular alignment purpose, e.g. contig or short/long-read alignment, can be used unchanged.
(In most of the known structural alignment problems, each point is the 3D coordinates of the C α atom, one per residue. Hence, a structure can be modeled for structural alignment purpose as a sequence of 3D points).
The algorithm does not require the adjustment or modification of the alignment scoring scheme(s) that is usually tuned for a particular alignment purpose, e.g. cross-species, contig or read alignments.
Similar(54)
The school also offers ballet "for alignment purposes and for muscular development," Ms. Ross said, referring to the underpinnings of good dance form.
For alignment purposes and in order to facilitate comparison to nuclear sputtering conditions, the system also includes a 5 keV Ar+ ion beam directed to the same sample area.
In those cases predicted sequences were used for alignment purposes.
For alignment purposes, the amino acids of the entire M2 helix can be numbered sequentially from N- to C-terminus (intracellular-to extracellular, 1'–28'; M243-A270 in α subunit).
We integrated a SD-OCT with the dual- wavelength PAOM for optical alignment purposes [ 1].
These characteristics are important to know for word alignment purposes but also contain useful information about the terminology systems themselves.
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