The source tree
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"If you can conceive of a bioinformatics job that could be done, it probably already has been done in the kent source tree." (Hiram)
- Tools to explore the source tree:
- you can use ctags to index the source tree
- and use cscope to search in the source tree (any better ideas for searching?)
- mc to explore the source tree
- Hiram has a [nice list] created from the help infos
- src/product: Very important info on how to install the gbdb on your own computer
- src/utils: Various small tools, not especially related to a particular genome
- src/hg: Almost all tools related to any kind of genome
- src/hg/mousestuff: everything related to chaining, netting and whole-genome alignments
- /src/hg/makeDb: Tools and scripts (!) that were used to load data into the databases. Most of them in subdirs here in the format hgLoadx with x for maf/bed/wiggle/axt/net/chain/out/etc. If you understand these, you understand how to build your own genome browser. :-)
- UCSC terms:
- axt: some aligner, maybe called faAlign? Also the name of a file format for local alignments.
- psl file: A format for local alignment hits used by blat. (axt and psl are convertible with axtToPsl)
- chaining: post-treating local alignments to see if two aligned regions that were located close on the query are located close to each other on the subject.
- chain file: positions of identical nucleotides
- netting: post-treating chains to group together many chains into one long alignment.
- net file: positions of alignable regions
- Xa file: ? pslToXa ?
Cool Files:
- /kent/src/oneShot/testScripters: cool collection of scripts to test the speed of various languages, result as expected: C with Jim's libs is much faster than anything else
