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gc (version 1.0)

This program reads DNA or RNA sequences and writes their length (in bases),
absolute GC content, and GC ratio (i.e. GC content devided by sequence length)
to standard output. The sequences are usually read from an input file. If no filename
is given, gc works in interactive mode. In this mode the user is prompted to type in
a sequence, and the calculated data are put out immediately. You can leave the
interactive mode (and exit the program) by entering @.

See the manual for a more detailed description of this tool.

Download

The program: gc.exe (248 KB)
Example input files: example_seqs.txt (1 KB) example_seqs_w_IDs.txt (1 KB)

Examples

With input sequences like these:

ttcgccctgctactaacacg

agataacagcaggatttctt
ggatcgcaggatctcagtca
gtgaccctccttccagtccg
gaattccatatcccttccaa
agaccgggctccgcacctgt
cttcacatacaaaattaatc
gtccttcccgcggtttctac


gc produces a table like this:

sequence        length  number_GC       GC_ratio
gtacttccttaaacgacgcagg  22      11      0.5
ggcggtaaaagaatcttggctg  22      11      0.5
catatctcggcacacatgatgg  22      11      0.5
cttatcgctttatgaccggacc  22      11      0.5
gcttcggattaacagtgacgtg  22      11      0.5
caatgaaacactaggcgaggac  22      11      0.5
cttcacgattgccactttccac  22      11      0.5
cgtgtagcctttgtattcgtcc  22      11      0.5


An interactive session may look like this:

>gc
Enter sequence (@ to exit):
aaaaaaaaaaa
sequence        length  number_GC       GC_ratio
aaaaaaaaaaa     11      0       0

Enter sequence (@ to exit):
gcgcgcgcgcg
sequence        length  number_GC       GC_ratio
gcgcgcgcgcg     11      11      1

Enter sequence (@ to exit):
acgugcaugaccgauca
sequence        length  number_GC       GC_ratio
acggcagaccgaca  14      9       0.642857

Enter sequence (@ to exit):
@



last modification: Dec/05/2007

 
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