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

1. hmmer.janelia.org
Protein similarity web searches
and services using HMMER
Rob Finn

2. hmmer.janelia.org
Use 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. hmmer.janelia.org
HMMER vs BLAST
H
HMMER
R BLAST
T
Program
m phmmer
r blastp
p
Query
y Single sequence
e e
Target
t Sequence database
e e
Databasee
Programm hmmscan
n rpsblast
t
Query
y Single sequence
e e
Target
t Profile HMM database,
e M , PSSM database,
M ,
Databasee e.g. Pfam
. m e.g. CDD
. D
Programm hmmsearch h psi-blast
t
Query
y Profile HMM
e M PSSM
M
Target
t Sequence database
e e
Databasee
Programm jackhmmer
r psi-blast
t
Query
y Single sequence
e e
Target
t Sequence database
e e
Database
e
Modified from: S. R. Eddy
PLoS Comp. Biol., 7:e1002195, 2011.

4. hmmer.janelia.org
Fast 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. hmmer.janelia.org
Visualization of Results – By Score

6. hmmer.janelia.org
Visualization of Results – By Score

7. hmmer.janelia.org
Visualization of Results – By Taxonomy

8. hmmer.janelia.org
Visualization of Results – By
Domain

9. hmmer.janelia.org
Acknowledgements
Jody Clements
Travis Wheeler
Sean Eddy
@hmm3r
http://cryptogenomicon.org/ Poster 160
hmmer@janelia.hhmi.org
hmmer.janelia.org