2012 Biocuration - Protein similarity searches using HMMER

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Overview of the HMMER website interface for performing protein similarity searches.

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2012 Biocuration - Protein similarity searches using HMMER

  1. 1. hmmer.janelia.orgProtein similarity web searchesand services using HMMERRob Finn
  2. 2. hmmer.janelia.orgUse of HMMER• Widely used by protein family databases • Use ‘seed’ alignments• Until 2010 • Computationally expensive • Restricted to HMMs constructed from multiple sequence alignments• Command line application SeqDB
  3. 3. hmmer.janelia.orgHMMER vs BLASTH HMMER R BLAST TProgram m phmmer r blastp pQuery y Single sequence e eTarget t Sequence database e eDatabaseeProgramm hmmscan n rpsblast tQuery y Single sequence e eTarget t Profile HMM database, e M , PSSM database, M ,Databasee e.g. Pfam . m e.g. CDD . DProgramm hmmsearch h psi-blast tQuery y Profile HMM e M PSSM MTarget t Sequence database e eDatabaseeProgramm jackhmmer r psi-blast tQuery y Single sequence e eTarget t Sequence database e eDatabase e Modified from: S. R. Eddy PLoS Comp. Biol., 7:e1002195, 2011.
  4. 4. hmmer.janelia.orgFast Web Searches• Parallelized searches across compute farm • Average query returns ~1 sec• Range of sequence databases • Large Comprehensive • Curated / Structure • Metagenomics • Representative Proteomes• Family Annotations hmmer.janelia.org • Pfam• Batch and RESTful API • Automatic and Human interface
  5. 5. hmmer.janelia.orgVisualization of Results – By Score
  6. 6. hmmer.janelia.orgVisualization of Results – By Score
  7. 7. hmmer.janelia.orgVisualization of Results – By Taxonomy
  8. 8. hmmer.janelia.orgVisualization of Results – ByDomain
  9. 9. hmmer.janelia.orgAcknowledgementsJody ClementsTravis WheelerSean Eddy @hmm3r http://cryptogenomicon.org/ Poster 160 hmmer@janelia.hhmi.org hmmer.janelia.org

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