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UNIT 6.12 Using OrthoMCL to Assign Proteins to OrthoMCL-DB Groups or to Cluster Proteomes Into New Ortholog Groups

  1. Steve Fischer1,3,
  2. Brian P. Brunk1,2,
  3. Feng Chen4,
  4. Xin Gao1,2,
  5. Omar S. Harb1,2,
  6. John B. Iodice1,3,
  7. Dhanasekaran Shanmugam2,
  8. David S. Roos2,
  9. Christian J. Stoeckert Jr.1,3

Published Online: 1 SEP 2011

DOI: 10.1002/0471250953.bi0612s35

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Fischer, S., Brunk, B. P., Chen, F., Gao, X., Harb, O. S., Iodice, J. B., Shanmugam, D., Roos, D. S. and Stoeckert, C. J. 2011. Using OrthoMCL to Assign Proteins to OrthoMCL-DB Groups or to Cluster Proteomes Into New Ortholog Groups. Current Protocols in Bioinformatics. 35:6.12:6.12.1–6.12.19.

Author Information

  1. 1

    Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania

  2. 2

    Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania

  3. 3

    Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania

  4. 4

    Bayer Business and Technology Services, Bayer Healthcare Pharmaceuticals, Wayne, New Jersey

Publication History

  1. Published Online: 1 SEP 2011
  2. Published Print: SEP 2011
Table 6.12.1. Troubleshooting Guide for Basic Protocol 1
ProblemPossible causeSolution
Receiving mail that says your job failedYou submitted an invalid FASTA fileRead the FASTA format description at http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml. Submit a valid FASTA file
 You submitted a FASTA file with non-unique IDs per sequenceGive each sequence a unique ID, and resubmit.