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duplex2hairpin (version 1.0)This program reads pairs of nucleic acid sequences from an input file, connects them viaa 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
ExampleThis 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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