Notes on methods used by Blaxter, XXXXX, Science, XXXXX (1998)

C. elegans predicted genes in WormPep (release 14) were processed using the Pfam domainer 1.6 system (E.L.L. Sonnhammer, D. Kahn, Protein Science 3, 482-492) and the resulting domains (groups of =FF2 protein segments with significant similarity to each other) were compared to SwissProt 35 and SPTREMBL. All domains with significant similarities to non-nematode proteins were eliminated, leaving 409 apparently nematode-specific domains containing from 58 to 2 members. The analysis was performed by S.J. Jones. A previous analysis of a WormPep dataset encompassing about one third of the complete dataset identified many of these domains (E.L.L. Sonnhammer, R. Durbin, Genomics 46:200-216 (1997)).