HMMER Profile Alignment
Align protein or nucleotide sequences to a profile HMM with HMMER.
Overview
Align protein, DNA, or RNA sequences to a profile hidden Markov model with HMMER hmmalign. Each sequence is aligned independently to the profile's consensus match states to produce a profile-anchored multiple sequence alignment.
Run HMMER Profile Alignment on Neurosnap
The HMMER Profile Alignment online webserver allows anybody with a Neurosnap account to run and access HMMER Profile Alignment, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- Aligns protein, DNA, or RNA sequences to one HMMER profile HMM.
- Produces profile-anchored multiple sequence alignments in Stockholm and aligned FASTA formats.
- Preserves posterior-probability and reference-column annotations in Stockholm output.
- Optionally includes the original alignment used to build the profile with HMMER map alignment.
- Optionally trims nonhomologous terminal residues outside the profile alignment.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access HMMER Profile Alignment using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using HMMER Profile Alignment in publications or research outputs.
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Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011;7(10):e1002195. doi:10.1371/journal.pcbi.1002195. |
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HMMER development team. HMMER: biological sequence analysis using profile hidden Markov models. https://hmmer.org/. |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |