User:Wayne Decatur/Sequence analysis tools: Difference between revisions
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== RNA Structure Analysis== | == RNA Structure Analysis== | ||
* [http://eddylab.org/infernal/ Infernal] - A downloadable program | * [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]) | ||
== Sequence Logo Generation == | == Sequence Logo Generation == | ||
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*[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756450/#CR3 SEQOTRON] - Mac Software for adjusting sequence alignments by hand. Unfortunately it discards the conservation data if it is there in input. Haven't found a way to put it back in the output other than use [http://www.bioinformatics.nl/ `cons` alignment consensus program and many others at EMBOSS explorer website] | *[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756450/#CR3 SEQOTRON] - Mac Software for adjusting sequence alignments by hand. Unfortunately it discards the conservation data if it is there in input. Haven't found a way to put it back in the output other than use [http://www.bioinformatics.nl/ `cons` alignment consensus program and many others at EMBOSS explorer website] | ||
Windows equivalent is [http://www.mbio.ncsu.edu/BioEdit/page2.html here] but I have '''NOT''' tried it. | Windows equivalent is [http://www.mbio.ncsu.edu/BioEdit/page2.html here] but I have '''NOT''' tried it. | ||
==Python-based utilities== | |||
* [[https://github.com/fhcrc/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. | |||
==My own sequence work-related code== | ==My own sequence work-related code== | ||
