Difference between revisions of "UCSC"
Moskalenko (talk | contribs) m (Text replace - "<!--Choose sections to enable - OPTIONAL--> |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->" to "") |
Moskalenko (talk | contribs) m (Text replace - "|{{#vardefine:intel|}} <!-- E.g. "11.1" --> |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->" to "") |
||
| Line 8: | Line 8: | ||
|{{#vardefine:url|http://genomewiki.cse.ucsc.edu/index.php/The_source_tree}} | |{{#vardefine:url|http://genomewiki.cse.ucsc.edu/index.php/The_source_tree}} | ||
<!--Compiler and MPI settings - OPTIONAL --> | <!--Compiler and MPI settings - OPTIONAL --> | ||
| − | + | ||
| − | |||
|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
Revision as of 17:53, 10 August 2012
|
|
Description
Kent source utilities are based on the code originally developed by Jim Kent for the UCSC genome browser. They include programs for sorting, splitting, or merging fasta sequences; record parsing and data conversion using GenBank, fasta, nib, and blast data formats; sequence alignment; motif searching; hidden Markov model development; and much more. Library subroutines are available for everything from managing C data structures such as linked lists, balanced trees, hashes, and directed graphs to developing routines for SQL, HTML, or CGI code. Additional library functions are available for biological sequence and data manipulation tasks such as reverse complementation, codon and amino acid lookup and sequence translation, as well as functions specifically designed for extracting, loading, and manipulating data in the UCSC Genome Browser Databases.
Required Modules
Serial
- kent