Why do I get different alignments when importing a homolog into the Prime Structure Prediction panel and when selecting the same homolog in the results of a search for homologs?

When you import a homolog into the Prime Structure Prediction panel, a ClustalW job is run to align the template to the query, rather than a Blast job. When you run a search for homologs, Blast is used for the search and the alignment. For systems with high sequence identity, there will probably not be large differences, however, for systems with lower sequence identities, the differences may be larger. In particular, the scores will be different because BLAST assesses the importance of the different regions of the sequence, and won't include regions it considers unimportant in the score it calculates.

Keywords: Prime, structure prediction

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