Computational protocol: C. elegans Agrin Is Expressed in Pharynx, IL1 Neurons and Distal Tip Cells and Does Not Genetically Interact with Genes Involved in Synaptogenesis or Muscle Function

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Protocol publication

[…] Protein architecture was analysed with SMART (EMBL, ), and with Blast at ExPASy . Several overlapping domains were predicted, but in this report only a representative structure is presented based on the similarity to the vertebrate orthologues. Laminin G domains of C. elegans agrin were used as a query in myHits against Swissprot, Trembl and Refseq. After the analysis of a more extensive alignment, the most informative Swissprot hits were selected. Visualization was done in Jalview, using Zappo colors without conservation threshold, to analyze subgroups . Alignments were submitted to the Boxshade server at Pasteur (http://bioweb.pasteur.fr/seqanal/interfaces/boxshade.html) for producing the greyscale shading. Pairwise comparison of sequences (% identity/% similarity) was performed using Smith Waterman alignments (as implemented in water, a tool in the EMBOSS package; . The homology searches between fragments of C. elegans agrin sequence and chicken agrin were done at myHits (SIB) using iterative PSI-BLAST searches . The C. elegans fragment composed of 2 lamG domains yielded different Blast scores for alternatively spliced chicken agrin isoforms (Swissprot), which was due to the presence, or absence, of the spliced exons. The alignments of the conserved alternative splicing site were produced by Blast at ExPASy. […]

Pipeline specifications

Software tools MyHits, Jalview, BoxShade, EMBOSS, BLASTP
Databases ExPASy
Applications Protein sequence analysis, Proteome data visualization
Organisms Caenorhabditis elegans