Algoritms

[Michael Bunnemeyer]

Hello,

The number of genomic tools, a.k.a. algorithms is continuing to increase. Do you know if anyone at UCSC or elsewhere is keeping track of what is available, and if this information is published, with the proper indications for the use of each algorithm?

Thank you very much.

Michael G. Bunnemeyer, MD

[Brian Lee]

Dear Michael,

Thank you for using the UCSC Genome Browser and your question about our genomic tools.

There are a number of resources to review that can be found on our publication pages that describe our new tools, http://genome.ucsc.edu/goldenPath/pubs.html, specifically an annual Nucleic Acids Research Database issue that summarizes our major enhancements:

The UCSC Genome Browser database: 2016 update. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702902/

The UCSC Genome Browser database: 2015 update. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383971

Ongoing software changes are also described in our Genome Browser Software Features wikipage for each tri-weekly release throughout the year: http://genomewiki.ucsc.edu/index.php/Genome_Browser_Software_Features

We also maintain an open source repository of our source code available through git, http://genome.ucsc.edu/admin/git.html, where notes are recorded about each change to the code.

We also provide precompiled tools that are available in the appropriate directory for different operating systems, as well as a userApps source with versioned histories and a process to make updates to the binary tools:

http://hgdownload.soe.ucsc.edu/admin/exe/

http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genomics Institute

--