Alignment method manual

Most sequence alignment methods are automated, but some are performed manually. Both the automated and the manual alignment of multiple chains is a challenging problem because of the myriad of alignment possibilities. The number of combinations for alignment is determined by raising the number of sequences by the number of amino acid residues of the longest sequence (Equation [1]). 

Alignment method (gap treatment) + method of analyses 1. Manual + MP ratchet 2. DO 3. DO (gaps as ) + MP ratchet 4. Manual + ML 1. Manual + MP ratchet (incl. only molecular data) 2. DO (incl. only molecular data) 3. DO (incl. morphology + molecular data) 1. Manual + MP ratchet... 

However, information concerning thermal rise is not available for all equipment. Generally, manufacturers of critical machinery, such as centrifugal air compressors and turbines, will include information relating to thermal rise in their installation manuals in the section dealing with alignment. When not available, the only method to determine the exact amount of compensation necessary to correct for thermal rise is referred to as a hot alignment check . 

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

Pharmacophores for opioid receptors have been determined using a custom implementation of the MNMM method [46], and cannabinoid receptors have been studied using Yak [47], Pharmacophores for the leukotriene receptors have been determined one for cysLT(l), developed using Catalyst with manual manipulation, was used to perform the alignment prior to a CoMFA model [48], and one for the... 

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