Difference between revisions of "UCSC"

Revision as of 18:57, 26 March 2020

Description

USCS genome browser utilities include programs for sorting, splitting (faSpli), 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

modules documentation

Serial

ucsc

System Variables

HPC_UCSC_DIR - installation directory

@@ Line 3: / Line 3: @@
 [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
 {|<!--Main settings - REQUIRED-->
-|{{#vardefine:app|kent}}
+|{{#vardefine:app|ucsc}}
 |{{#vardefine:url|http://genomewiki.cse.ucsc.edu/index.php/The_source_tree}}
 |{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
@@ Line 18: / Line 18: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-Kent source utilities are based on the code originally developed by Jim Kent for the UCSC genome browser. They include programs for sorting, splitting (faSpli), 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.
+USCS genome browser utilities include programs for sorting, splitting (faSpli), 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.
-The ''kent'' module provides access to over 600 binaries with some of the more popular being wigToBigWig, faSplit, and faToTWoBit.
 <!--Modules-->
 ==Required Modules==