User:Wayne Decatur/Sequence analysis tools: Difference between revisions
From Proteopedia
Jump to navigationJump to search
add rna tools |
m fix wikitext |
||
| (13 intermediate revisions by the same user not shown) | |||
| Line 64: | Line 64: | ||
==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== | ||
| Line 82: | Line 90: | ||
==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 == | |||
[http://1002genomes.u-strasbg.fr/news/news.html 1011 Saccharomyces cerevisiae genomes ], associated with [https://www.ncbi.nlm.nih.gov/pubmed/29643504 Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Peter J, De Chiara M, Friedrich A, Yue JX, Pflieger D, Bergström A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G, Schacherer J. Nature. 2018 Apr;556(7701):339-344. doi: 10.1038/s41586-018-0030-5. Epub 2018 Apr 11. PMID: 29643504]. | |||
[ | [http://www.y1000plus.org 332 budding yeasts ] associated with [https://www.ncbi.nlm.nih.gov/pubmed/30415838 Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A. Cell. 2018 Nov 29;175(6):1533-1545.e20. doi: 10.1016/j.cell.2018.10.023. Epub 2018 Nov 8. PMID: 30415838]. ([https://figshare.com/articles/Tempo_and_mode_of_genome_evolution_in_the_budding_yeast_subphylum/5854692 Figshare corresponding to the paper]) | ||
https://figshare.com/articles/Tempo_and_mode_of_genome_evolution_in_the_budding_yeast_subphylum/5854692] | |||
http://fungalgenomes.org/ | http://fungalgenomes.org/ | ||
| Line 122: | Line 129: | ||
== 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 == | ||
