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URL: https://dx.doi.org/10.17504/protocols.io.ehfbb3n

Authors: Bonnie Hurwitz, Ken Youens-Clark

Group: VERVE Net, Hurwitz Lab

Summary: PCPipe is a protein-clustering tool.  The input is a set of ORFs and a FASTA file with already clustered ORFs. The process entails:Use cd-hit-2d to compare the input peptides to previously clustered proteinsThe result is a file with input proteins that clustered to existing clusters and those that did notUse the unclustered peptides and self-cluster them via cd-hitTake a representative sequence from each novel cluster, and use "blastp" to compare to SIMAP.Use the resulting SIMAP "feature_id" to look up the SIMAP features, merging the query results with the protein ID into a tab-delimited annotations fileProvide the user with two cluster files and the annotations for the new clusters based on the representative sequenceCode is freely available at Github.

Affiliations: University of Arizona, University of Arizona

Version: 1

Publication Date: 2016

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