Text Mining for Biocuration of Bacterial Infectious Diseases
2012 Biocuration - Protein similarity searches using HMMER
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Transcript of 2012 Biocuration - Protein similarity searches using HMMER
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Protein similarity web searches and services using HMMERRob Finn
hmmer.janelia.org
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Use of HMMER • Widely used by protein family
databases• Use ‘seed’ alignments
SeqDB
hmmer.janelia.org
• Until 2010• Computationally expensive• Restricted to HMMs constructed from
multiple sequence alignments
• Command line application
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HMMER vs BLASTH
HMMERR BLASTT
Programm phmmerr blastpp
Queryy Singlee sequencee
TargettDatabasee
Sequencee databasee
Programm hmmscann rpsblastt
Queryy Singlee sequencee
TargettDatabasee
Profilee HMMM database,,e.g.. Pfamm
PSSMM database,,,e.g.. CDDD
Programm hmmsearchh psi-blasttt
Queryy Profilee HMMM PSSMM
TargettDatabasee
Sequencee databasee
Programm jackhmmerr psi-blastt
Queryy Singlee sequencee
TargettDatabasee
Sequencee databaseee
hmmer.janelia.org
Modified from: S. R. EddyPLoS Comp. Biol., 7:e1002195, 2011.
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• Parallelized searches across compute farm• Average query returns ~1 sec
• Range of sequence databases• Large Comprehensive• Curated / Structure• Metagenomics• Representative Proteomes
• Family Annotations• Pfam
• Batch and RESTful API• Automatic and Human interface
hmmer.janelia.orghmmer.janelia.org
Fast Web Searches
hmmer.janelia.org
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Visualization of Results – By Score
hmmer.janelia.org
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Visualization of Results – By Score
hmmer.janelia.org
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Visualization of Results – By Taxonomy
hmmer.janelia.org
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Visualization of Results – By Domain
hmmer.janelia.org
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Acknowledgements
hmmer.janelia.org
Jody Clements
Travis Wheeler
Sean Eddy
@hmm3r
http://cryptogenomicon.org/
hmmer.janelia.org