hmmer (cloudIFB)
hmmer (cloudIFB) is a tool to search homologous protein sequences in public databases, such as Pfam. The hmmer (cloudIFB) algorithm uses Hidden Markov Models and produces graphical summaries of the search results.
Topic
Bioinformatics;Sequence analysis;Sequence sites, features and motifs;Proteins;Small molecules;Gene and protein families
Detail
Operation: Formatting;Multiple sequence alignment;Sequence profile generation;Format validation;Conversion;Sequence generation;Data retrieval;Statistical calculation;Database search;Formatting;Database search;Database search;Probabilistic sequence generation;Statistical calculation;Statistical calculation;Sequence database search;Formatting;Sequence database search;Database search;Sequence database search;Sequence similarity search;Multiple sequence alignment;Protein sequence analysis;Sequence database search;Protein feature detection
Software interface: Command-line user interface;Web user interface
Language: Perl;C
License: Other
Cost: Free
Version name: 3.3.2
Credit: Howard Hughes Medical Institute.
Input: FASTA
Output: -
Contact: sean@eddylab.org
Collection: -
Maturity: Mature
Publications
- Hidden Markov models
- Eddy SR. Hidden Markov models. Curr Opin Struct Biol. 1996 Jun;6(3):361-5.
- https://doi.org/0.1016/s0959-440x(96)80056-x
- PMID: 8804822
- PMC: -
- What is a hidden Markov model?
- Eddy SR. What is a hidden Markov model? Nat Biotechnol. 2004 Oct;22(10):1315-6.
- https://doi.org/10.1038/nbt1004-1315
- PMID: 15470472
- PMC: -
- Maximum discrimination hidden Markov models of sequence consensus
- Eddy SR, Mitchison G, Durbin R. Maximum discrimination hidden Markov models of sequence consensus. J Comput Biol. 1995 Spring;2(1):9-23.
- https://doi.org/10.1089/cmb.1995.2.9
- PMID: 7497123
- PMC: -
- Profile hidden Markov models
- Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14(9):755-63.
- https://doi.org/10.1093/bioinformatics/14.9.755
- PMID: 9918945
- PMC: -
- nhmmer: DNA homology search with profile HMMs
- Wheeler TJ, Eddy SR. nhmmer: DNA homology search with profile HMMs. Bioinformatics. 2013 Oct 1;29(19):2487-9.
- https://doi.org/10.1093/bioinformatics/btt403
- PMID: 23842809
- PMC: PMC3777106
- HMMER web server: interactive sequence similarity searching.
- Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W29-37.
- https://doi.org/10.1093/nar/gkr367
- PMID: 21593126
- PMC: PMC3125773
- Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
- Mistry J, Finn RD, Eddy SR, Bateman A, Punta M. Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res. 2013 Jul;41(12):e121.
- https://doi.org/10.1093/nar/gkt263
- PMID: 23598997
- PMC: PMC3695513
- A probabilistic model of local sequence alignment that simplifies statistical significance estimation
- Eddy SR. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol. 2008 May 30;4(5):e1000069.
- https://doi.org/10.1371/journal.pcbi.1000069
- PMID: 18516236
- PMC: PMC2396288
- Accelerated Profile HMM Searches
- Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011 Oct;7(10):e1002195.
- https://doi.org/10.1371/journal.pcbi.1002195
- PMID: 22039361
- PMC: PMC3197634
- Hidden Markov model speed heuristic and iterative HMM search procedure
- Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics. 2010 Aug 18;11:431.
- https://doi.org/doi: 10.1186/1471-2105-11-431
- PMID: 20718988
- PMC: PMC2931519
- A new generation of homology search tools based on probabilistic inference
- Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009 Oct;23(1):205-11.
- https://doi.org/keep-hmmer
- PMID: 20180275
- PMC: -
Download and documentation
Documentation: http://eddylab.org/software/hmmer/Userguide.pdf
Home page: http://hmmer.janelia.org/
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