User:Wayne Decatur/Sequence analysis tools: Difference between revisions
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* [http://biit.cs.ut.ee/gprofiler/ ProViz] - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. | * [http://biit.cs.ut.ee/gprofiler/ ProViz] - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. | ||
* [http://prody.csb.pitt.edu/index.html ProDy Project] - "ProDy is a free and open-source Python package for protein structural dynamics analysis". Looks like it does protein sequence analysis too and working with PDB files. | * [http://prody.csb.pitt.edu/index.html ProDy Project] - "ProDy is a free and open-source Python package for protein structural dynamics analysis". Looks like it does protein sequence analysis too and working with PDB files. | ||
==Aligning== | |||
* [https://github.com/fomightez/msucle-binder Muscle-binder - Launchable Jupyter environment for running command line-based Muscle via Binder.]. That page also links to the main MUSCLE resources there. | |||
==BLAST+== | ==BLAST+== | ||
* [https://github.com/fomightez/blast-binder Blast-binder - Launchable Jupyter environment for running command line-based BLAST via Binder.]. That page also links to the main BLAST resources there. The launched notebooks illustrate ways to easily work with the output in Python. | * [https://github.com/fomightez/blast-binder Blast-binder - Launchable Jupyter environment for running command line-based BLAST via Binder.]. That page also links to the main BLAST resources there. The launched notebooks illustrate ways to easily work with the output in Python. | ||
==Circos== | |||
* [https://github.com/fomightez/circos-binder Circos on Jupyter] - Circos in your browser-based Jupyter enviroment served from MyBinder.org. Circos so it is actively available in a browser with one click to launch Jupyter environment for Circos via Binder. That page also links to the main Circos resources there. The launched notebooks illustrate ways to easily work with the output in Python. | |||
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* [http://sequenceconversion.bugaco.com/converter/biology/sequences/clustal_to_fasta.php Sequence conversion Provided by bugaco.com] - a lot of conversion choices with easy interface. When I had interleaved clustal format it converted nicely to a straight fasta listing for the sequence for every organism. | * [http://sequenceconversion.bugaco.com/converter/biology/sequences/clustal_to_fasta.php Sequence conversion Provided by bugaco.com] - a lot of conversion choices with easy interface. When I had interleaved clustal format it converted nicely to a straight fasta listing for the sequence for every organism. | ||
* [http://toolkit.tuebingen.mpg.de/reformat Reformat utility of Max Planck Institute for Developmental Biology Bioinformatics Toolkit] converts sequences or multiple sequence alignments to various forms. | * [http://toolkit.tuebingen.mpg.de/reformat Reformat utility of Max Planck Institute for Developmental Biology Bioinformatics Toolkit] converts sequences or multiple sequence alignments to various forms. | ||
* [https://www.hiv.lanl.gov/content/sequence/FORMAT_CONVERSION/form.html?sample_input=1 Format Converter] - converts nucleotide and protein sequences in various formats to a lot of other formats. | |||
* [http://bioinformatics.org/sms2/three_to_one.html Three to One] converts three letter amino acid sequence translations to single letter translations. | * [http://bioinformatics.org/sms2/three_to_one.html Three to One] converts three letter amino acid sequence translations to single letter translations. | ||
* [http://bioinformatics.org/sms2/one_to_three.html One to Three] converts single letter amino acid sequence translations to three letter translations. | * [http://bioinformatics.org/sms2/one_to_three.html One to Three] converts single letter amino acid sequence translations to three letter translations. | ||
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* [http://biit.cs.ut.ee/gprofiler/gconvert.cgi g:Convert] - Gene ID Converter. Handles yeast and a very large list of other organisms. | * [http://biit.cs.ut.ee/gprofiler/gconvert.cgi g:Convert] - Gene ID Converter. Handles yeast and a very large list of other organisms. | ||
* [https://github.com/fhcrc/seqmagick seqmagick-An imagemagick-like frontend to Biopython SeqIO], can convert from fasta to phylip, etc. | * [https://github.com/fhcrc/seqmagick seqmagick-An imagemagick-like frontend to Biopython SeqIO], can convert from fasta to phylip, etc. | ||
* [Reverse and/or reverse complement DNA sequences that handles degenerate bases ](http://arep.med.harvard.edu/labgc/adnan/projects/Utilities/revcomp.html | |||
==Random sequence generators== | ==Random sequence generators== | ||
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* http://emboss.sourceforge.net/ - shuffleseq from EMBOSS shuffles a set of sequences maintaining composition. | * http://emboss.sourceforge.net/ - shuffleseq from EMBOSS shuffles a set of sequences maintaining composition. | ||
==Extract physico-chemical data from Protein or DNA sequences== | |||
* [https://www.iitm.ac.in/bioinfo/SBFE/index.html Seq2Feature webserver] is a comprehensive web-based feature extraction tool which computes protein and DNA sequence driven features. It can calculate 252 protein- based and 42 DNA- based descriptors. Major protein sequence based descriptors include physico-chemical, energetic and conformational properties, mutation matrices and contact potentials. There is a corresponding article [https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btz432/5499130?redirectedFrom=fulltext here]. | |||
==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 == | |||
[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]) | |||
http://fungalgenomes.org/ | http://fungalgenomes.org/ | ||
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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/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 == | ||
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* [https://github.com/fhcrc/seqmagick seqmagick-An imagemagick-like frontend to Biopython SeqIO]. For example, it can convert from fasta to phylip, remove gaps from a fasta-formatted sequence, and describe all FASTA files in the current directory. Requires Biopython. | * [https://github.com/fhcrc/seqmagick seqmagick-An imagemagick-like frontend to Biopython SeqIO]. For example, it can convert from fasta to phylip, remove gaps from a fasta-formatted sequence, and describe all FASTA files in the current directory. Requires Biopython. | ||
* see also on this page 'Binder'-related items as I usually have | * see also earlier on this page 'Binder'/notebook-related items as I usually have worked out Python code to shuttle other command-line based software output to Python and notebook-related items [https://github.com/fomightez/sequencework here] as I sometimes demonstrate script usage in launchable notebooks | ||
==My own sequence work-related code== | ==My own sequence work-related code== | ||
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* [https://github.com/fomightez/UGENE_help Working with UGENE software analysis software] | * [https://github.com/fomightez/UGENE_help Working with UGENE software analysis software] | ||
* [https://github.com/fomightez/yeastmine Working with Yeastmine] | * [https://github.com/fomightez/yeastmine Working with Yeastmine] | ||
* see also on this page 'Binder'-related items as I usually have worked out Python code to shuttle other command-line based software output to Python | * see also earlier on this page 'Binder'/notebook-related items as I usually have worked out Python code to shuttle other command-line based software output to Python and notebook-related items [https://github.com/fomightez/sequencework here] as I sometimes demonstrate script usage in launchable notebooks | ||
* see also [https://github.com/fomightez/ My Github] | |||
