User:Wayne Decatur/Sequence analysis tools - Revision history

Wayne Decatur: fix wikitext

2021-01-11T19:45:17Z

fix wikitext

← Older revision		Revision as of 19:45, 11 January 2021
Line 136:		Line 136:
	== Analyze DNA curvature==		== 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.		* [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 ==

Wayne Decatur: try to fix wikitext

2021-01-11T19:44:40Z

try to fix wikitext

← Older revision		Revision as of 19:44, 11 January 2021
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 ~~avialble~~ 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])		* [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.)

	* [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==		== Analyze DNA curvature==

	* [https://github.com/fomightez/bendit-binder bendit-binder] -se 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.		* [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 ==

Wayne Decatur: fix wikitext

2021-01-11T19:42:44Z

fix wikitext

← Older revision		Revision as of 19:42, 11 January 2021
Line 131:		Line 131:
	* [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 avialble 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])		* [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 avialble 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 ] - (~~preiously know~~ 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.)		* [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==		== 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.		* [https://github.com/fomightez/bendit-binder bendit-binder] -se 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 ==

Wayne Decatur: add some more of my recent resources

2021-01-11T17:50:42Z

add some more of my recent resources

← Older revision		Revision as of 17:50, 11 January 2021
Line 132:		Line 132:

	* [https://github.com/mmagnus/rna-tools/blob/master/index-of-tools.md rna-tools ] - (preiously know 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.)		* [https://github.com/mmagnus/rna-tools/blob/master/index-of-tools.md rna-tools ] - (preiously know 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 ==

Wayne Decatur: /* Nucleic acid system building */

2020-09-22T20:55:12Z

Nucleic acid system building

← Older revision		Revision as of 20:55, 22 September 2020
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." Seems to be able to do melting temperature and free energy calculations as well, etc..		* [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..

Wayne Decatur: /* Pattern Matching */

2020-09-22T20:49:57Z

Pattern Matching

← Older revision		Revision as of 20:49, 22 September 2020
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>

	* [~~HMMER: biosequence analysis using profile hidden Markov models~~ http://hmmer.org/publications.html]		* [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==

Wayne Decatur: /* Nucleic acid system building */

2020-09-22T20:49:32Z

Nucleic acid system building

← Older revision		Revision as of 20:49, 22 September 2020
Line 91:		Line 91:

	==Nucleic acid system building==		==Nucleic acid system building==
	* [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 ==

Wayne Decatur: /* Pattern Matching */

2020-09-22T20:48:32Z

Pattern Matching

← Older revision		Revision as of 20:48, 22 September 2020
Line 67:		Line 67:

	==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==

Wayne Decatur: /* Orthology */

2020-09-22T20:45:27Z

Orthology

← Older revision		Revision as of 20:45, 22 September 2020
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
	* [~~HH-suite3 for sensitive protein sequence searching based on HMM-HMM alignment](~~https://github.com/soedinglab/hh-suite/wiki#building-customized-databases)		* [https://github.com/soedinglab/hh-suite/wiki#building-customized-databases HH-suite3 for sensitive protein sequence searching based on HMM-HMM alignment]

	==Pattern Matching==		==Pattern Matching==

Wayne Decatur: /* Orthology */

2020-09-22T20:43:15Z

Orthology

← Older revision		Revision as of 20:43, 22 September 2020
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
			* [HH-suite3 for sensitive protein sequence searching based on HMM-HMM alignment](https://github.com/soedinglab/hh-suite/wiki#building-customized-databases)

	==Pattern Matching==		==Pattern Matching==