Author: Rawlings, Neil D.
Title: A large and accurate collection of peptidase cleavages in the MEROPS database Document date: 2009_11_2
ID: 0rq0wdpq_17
Snippet: The UniProt accession for each substrate with a known cleavage site was used to search the UniRef50 database (clusters of sequences that have at least 50% sequence identity to the longest sequence) (28) . If a UniRef50 entry was found, then all the UniProt accessions included in that entry were extracted and the sequences retrieved from the UniProt database in FastA format. Short fragments were excluded and the remaining sequences were then align.....
Document: The UniProt accession for each substrate with a known cleavage site was used to search the UniRef50 database (clusters of sequences that have at least 50% sequence identity to the longest sequence) (28) . If a UniRef50 entry was found, then all the UniProt accessions included in that entry were extracted and the sequences retrieved from the UniProt database in FastA format. Short fragments were excluded and the remaining sequences were then aligned with MUSCLE (29), using the default parameters and performing two iterations over the complete alignment to minimize gaps. Because each UniRef50 entry contains sequences sharing 50% or more sequence identity, the program is very quick, and the resulting alignment approximates to an alignment of orthologues. However, some UniRef50 entries will also contain closely related paralogues.
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