User:Wayne Decatur/Sequence analysis tools: Difference between revisions
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==Orthology== | ==Orthology== | ||
* [http://eggnogdb.embl.de/#/app/home EggNOG] - A database of orthologous groups and functional annotation | * [http://eggnogdb.embl.de/#/app/home EggNOG] - A database of orthologous groups and functional annotation | ||
* [https://github.com/soedinglab/hh-suite/wiki#building-customized-databases HH-suite3 for sensitive protein sequence searching based on HMM-HMM alignment] | |||
==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> | |||
* [http://hmmer.org/publications.html HMMER: biosequence analysis using profile hidden Markov models] | |||
==Some sequence analysis but mostly OTHER== | ==Some sequence analysis but mostly OTHER== | ||
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==Nucleic acid system building== | ==Nucleic acid system building and DNA structure design== | ||
* [http://www.nupack.org/ NUPACK] - "NUPACK is a growing software suite for the analysis and design of nucleic acid systems." | * [http://www.nupack.org/ NUPACK] - "NUPACK is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems." Seems to be able to do melting temperature and free energy calculations as well, etc.. | ||
== Fungal Genome Resources == | == Fungal Genome Resources == | ||
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== RNA Structure Analysis== | == RNA Structure Analysis== | ||
* [http://eddylab.org/infernal/ Infernal] - A downloadable program fors equence analysis using profiles of RNA sequence based on [http://rfam.xfam.org/ Rfam]-associated covariance models and secondary structure consensus. The program can generate covariance models from RNA alignments as well. Binaries are | * [http://eddylab.org/infernal/ Infernal] - A downloadable program fors equence analysis using profiles of RNA sequence based on [http://rfam.xfam.org/ Rfam]-associated covariance models and secondary structure consensus. The program can generate covariance models from RNA alignments as well. Binaries are available for Mac, Windows, and Linux. ( [http://www.ncbi.nlm.nih.gov/pubmed/24008419?dopt=Abstract E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013). PMID: 24008419]) | ||
* [https://github.com/mmagnus/rna-tools/blob/master/index-of-tools.md rna-tools] - (previously known as ' rna-pdb-tools'): a toolbox to analyze sequences, structures and simulations of RNA. (Takes some navigating around to find what you want because a lot is there.) | |||
== Analyze DNA curvature== | |||
* [https://github.com/ | * [https://github.com/fomightez/bendit-binder bendit-binder] - use the [http://pongor.itk.ppke.hu/dna/bend_it.html#/bendit_intro Bend.it software] to predict DNA curvature from DNA sequences with the power of the Jupyter ecosystem served via MyBinder.org. | ||
== Sequence Logo Generation == | == Sequence Logo Generation == | ||
