Computational protocol: Genetic Suppression of Basement Membrane Defects in Caenorhabditis elegans by Gain of Function in Extracellular Matrix and Cell-Matrix Attachment Genes

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Protocol publication

[…] We performed alignments of LET-805 with other FNIII repeat-containing proteins using BLAST. The numbering of FNIII repeats in Figure S2 in File S1 is based on reanalysis with additional protein domain prediction algorithms; sequence alignments use ClustalX. Protein domain graphics were generated using IBS software (), based on domains identified in the conserved domain database of the National Center for Biotechnology Information (). Predicted structures of subsets of the LET-805 FNIII repeats were generated using SWISS-MODEL (). Models in Figure S3 in File S1 are based on the human IL-6 receptor FNIII repeats. […]

Pipeline specifications

Software tools Clustal W, SWISS-MODEL
Databases CDD
Application Protein structure analysis
Organisms Caenorhabditis elegans