User:Wayne Decatur/Sequence analysis tools: Difference between revisions
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==Pattern Matching== | ==Pattern Matching== | ||
* [https://github.com/fomightez/patmatch-binder patmatch-binder- Launchable Jupyter environment for running command line-based PatMatch via Binder]. That page also links to other sequence pattern matching resources. The launched notebooks illustrate ways to easily work with the output in Python. | * [https://github.com/fomightez/patmatch-binder patmatch-binder- Launchable Jupyter environment for running command line-based PatMatch via Binder]. That page also links to other sequence pattern matching resources. The launched notebooks illustrate ways to easily work with the output in Python. | ||
* [https://github.com/soedinglab/hh-suite/wiki#building-customized-databases HH-suite3 for sensitive protein sequence searching based on HMM-HMM alignment] | |||
* [http://eddylab.org/infernal/ Infernal: inference of RNA alignments] | |||
<blockquote> Infernal builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence alignments.</blockquote> | |||
* [HMMER: biosequence analysis using profile hidden Markov models http://hmmer.org/publications.html] | |||
==Some sequence analysis but mostly OTHER== | ==Some sequence analysis but mostly OTHER== | ||
