User:Wayne Decatur/Sequence analysis tools: Difference between revisions
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m clarify I did at first mean above on this page |
m add some new tools |
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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+== | ||
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==Circos== | ==Circos== | ||
* [https://github.com/fomightez/circos-binder 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://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== | ||
