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CANADA: duplex2hairpin

duplex2hairpin (version 1.0)

This program reads pairs of nucleic acid sequences from an input file, connects them via
a linker sequence and writes the resulting sequences to standard output. This is useful
when you want to use a single stranded secondary structure prediction program like
RNAfold for predicting duplex formation of a pair of sequences. To this end, one
connects the two sequences of  interest with a linker sequence of non-pairing bases
which will form a hairpin loop with the two sequences forming the stem. You can also
add constraints for RNAfold to the output, forcing that program to allow only base pairs
between the two sequences, but not between bases of one and the same sequence.

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

Download

The program: duplex2hairpin.exe (248 KB)
Example input files: example_seqs.txt (1 KB) example_seqs_w_IDs.txt (1 KB)

Example

This tool can take pairs of these sequences from a file:

ttcgccctgctactaacacg
agataacagcaggatttctt
ggatcgcaggatctcagtca
gtgaccctccttccagtccg
gaattccatatcccttccaa
agaccgggctccgcacctgt
cttcacatacaaaattaatc
gtccttcccgcggtttctac

and link them to these sequences:

ttcgccctgctactaacacgnnnnnnnnnnnnnnnnagataacagcaggatttctt
ggatcgcaggatctcagtcannnnnnnnnnnnnnnngtgaccctccttccagtccg
gaattccatatcccttccaannnnnnnnnnnnnnnnagaccgggctccgcacctgt
cttcacatacaaaattaatcnnnnnnnnnnnnnnnngtccttcccgcggtttctac

last modification: Jun/20/2007

  
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