Computational protocol: CPNA-1, a copine domain protein, is located at integrin adhesion sites and is required for myofilament stability in Caenorhabditis elegans

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Protocol publication

[…] BLAST, using CPNA-1 as query against the C. elegans translated genome, was used to identify the complete set of copine containing proteins in this organism, as well as those in other organisms. PFAM was used to identify the copine domain boundaries and to identify other possible domains (e.g., C2 domains). The multisequence alignment of copine domains from C. elegans was performed using www.genome.jp/tools/clustalw/. To predict possible transmembrane helices in the copine family, we used the following programs: TMHMM Server v. 2.0 (www.cbs.dtu.dk/services/TMHMM-2.0), PRED-TMR (http://athina.biol.uoa.gr/PRED-TMR/input.html), and HMMtop (www.enzim.hu/hmmtop/server/hmmtop.cgi). […]

Pipeline specifications

Software tools Clustal W, TMHMM, PRED-TMR, HMMTOP
Databases Pfam
Application Membrane protein analysis
Organisms Caenorhabditis elegans
Diseases Lymphohistiocytosis, Hemophagocytic