User:Wayne Decatur/Sequence analysis tools: Difference between revisions
From Proteopedia
Jump to navigationJump to search
m fix wikitext |
|||
| (6 intermediate revisions by the same user not shown) | |||
| Line 76: | Line 76: | ||
<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> | <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 90: | 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 structures, devices, and 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 == | ||
| Line 129: | 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 ] - ( | * [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/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 == | ||
