New answers tagged sequence-analysis
I think it's like this: signatures: domains (which are detected using profiles) motifs = fingerprint = pattern Where motifs are short stretches of residu's which can be part of a domain, but don't have to be part of it. Domains are functional unitits of a proteïn (which thus can contain motifs).
Looking at the documentation you provide, I think that I can provide definitions for those terms as defined by EXPASY. Note that those definitions may just be an in-house system that EXPASY uses that you can't generalize to other databases for instance. First, in section I.C of the documentation, they write "The use of protein sequence patterns (or motifs) ...
At the command line: wget ftp://ftp.ensembl.org/pub/release-84/gtf/gasterosteus_aculeatus/Gasterosteus_aculeatus.BROADS1.84.gtf.gz gunzip Gasterosteus_aculeatus.BROADS1.84.gtf.gz Then in R: library(GenomicFeatures) txdb = makeTxDbFromGFF("Gasterosteus_aculeatus.BROADS1.84.gtf") hist(log10(width(unique(exons(txdb))))) # exons hist(log10(width(unique(...
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