UCSC¶

Description¶

USCSC Genome Browser utilities are based on the code originally developed by Jim UCSC 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.

Environment Modules¶

Run module spider ucsc to find out what environment modules are available for this application.

Environment Variables¶

HPC_UCSC_DIR - installation directory
HPC_UCSC_BIN - executable directory

Citation¶

If you publish research that uses ucsc you have to cite it as follows:

Gerardo Perez, Galt P Barber, Anna Benet-Pages, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S Hinrichs, Christopher M Lee, Luis R Nassar, Brian J Raney, Matthew L Speir, Marijke J van Baren, Charles J Vaske, David Haussler, W James Kent, Maximilian Haeussler, The UCSC Genome Browser database: 2025 update, Nucleic Acids Research, Volume 53, Issue D1, 6 January 2025, Pages D1243–D1249, https://doi.org/10.1093/nar/gkae974

Categories¶

genomics