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Download Orphea |
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Orphea manual page |
Synopsis:
orphea [-1] [-s] [-i pattern] [-x pattern] [-r] [-c cds_file] [-o output file]
FASTA_input_file [ARFF output file]
Input:
The input file can be a FASTA format file, a concatenation of many FASTA files; Using plain text or compressed with gzip.
Output:
The output file summarises the pseudo-knots found that are good candidates for FS-1. They are first searched in the direct strand (the input sequence) then, unless the -r switch is used, in the reverse complementary sequence.
The output looks like this:
where ``cand_NNN'' means FS-1 candidate number NNN, ``offset'' is the location in the input sequence where the PK has been found, the scores are those found for each stem.NC_00003 S.cerevisiae synthetised genome, 12000000 bases Direct strand cand_1: offset: 10297906 scores: stem1 = 157, stem2 = 38 GGGAAAUUUGAGUGGAUUCACGAAAUGAAUCCACCUCUUGGAUAUGUAAAAAUGGUGCCG *******....((((((((([[...)))))))))........................]] ... cand_42: offset: 6869568 scores: stem1 = 124, stem2 = 52 UUUUUUUCAACUUACAAAUCUGGAUCCACUUCCAGAUUUUUCAAGAAUUAUUUAUCCAAAUUGGA *******........((((((((([[[[..)))))))))......................]]]] Reverse complement cand_43: offset: 1891213 scores: stem1 = 129, stem2 = 82 GGGAAAACCCUUCCGAGGGCAAUUCCUCAACCGUGCUUCUCUAUAAAGGCCCAGGAAUCUACAAAUAACACGG *******.........((((..........[[[[[.............))))................]]]]] ... cand_102: offset: 10654018 scores: stem1 = 152, stem2 = 51 UUUUUUUCUCUUCACGGCGCUCUAAGUUUGAUUGGCCCAAACAUUCAUACGCCGUUGAACACCUUGUUGGACUUCAGAC *******......((((((......[[[[[[..................))))))..................]]]]]] ------------------------------------------------------------------------------- 102 PK found.
The candidate sequence is output starting from the slippery sequence up to the last base of the second stem. The pairings are shown in the next line, using the bracket/parenthesis notation.
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