dincarnato / SHAPEwarp

SHAPE-guided RNA structural homology search
GNU General Public License v3.0
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[!] No significant match with current search parameters problem #2

Closed sfsdfd62 closed 2 years ago

sfsdfd62 commented 2 years ago

Dear dincarnato, Greetings. Below is my input. After I feed this into SHAPEwarp, it says [!] No significant match with current search parameters.

Seq_33
TCCGTTGACCTTAAACGGTCGTGTGGGTTCAAGTCCCTCCACCCCCACGCCGGAAACGCAATAGCCGAAAAACAAAAAACAAAAAAAACAAAAAAAAAACCAAAAAAACAAAACACAGGCGCGCCAGTCCTACAATGCCGGCCCAGCCGTTCGGTGCGCGATTGGCTGCCGCTGCCACTTACGCGTCGCTCTTCCTCGTTTGCCCCTCGTGTTCATGGGAGCTCGTTTTCTTTTCCTCTAGGCAGAGAAGAGGCGATGGCGGCGATGGCATCTCTCGGCGCCCTGGCGCTGCTCCTGCTGTCCAGCGACTCGGACCGATGATCATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCACCCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGAAAAAACAAAAAACAAAACGGCTATTATGCGTTACCGGCGAGACGCTACGGACTTAAATAATT 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Could you tell me what might went wrong? Thank you very much!!!!

dincarnato commented 2 years ago

Dear sfsdfd62,

this is very vague. The message indicates that for your query there is no significant match returned. What database are you searching into? Do you expect to see matches? What parameter set are you using?

Best, Danny

sfsdfd62 commented 2 years ago

Dear dincarnato,

I used the default database and parameter, And I used RNAplfold to get the base-pairing probability. It seems that I should make my own database. But is it OK to use the base-pairing probability generated by RNAplfold to serve as the input? Thank you !!!!!!

Best, sfsdfd62

dincarnato commented 2 years ago

Dear sfsdfd62,

it would be good to understand what are you trying to achieve. Also, please read the SHAPEwarp manual to understand how the program works (https://shapewarp-docs.readthedocs.io/en/latest/) and, if you are searching for unpaired probabilities rather than SHAPE reactivities, I suggest you to look at the materials and methods of the original paper as the suggested parameters where indicated there.

Best, Danny

dincarnato commented 2 years ago

Hi sfsdfd62,

as there is no real problem with SHAPEwarp, I am gonna close this issue. Best,

Danny

sfsdfd62 commented 1 year ago

Dear dincarnato. I have read the paper, and I just don't know how to feed the probability into the SHAPEwarp. I noticed that SHAPE reacitivity could be displayed like: AGTGG 0.490,0.327,0.610,1.171,2.621 But the base pairing probability for RNA sequence is always a matrix, which means one nucleotide could have different probabilities with other nucleotides. What could be the input format for probabilities? I didn't see it in the doc or in the methods part. I would appreciated it if you could answer my stupid little question,which have troubled me for months... Best,

sfsdfd62

dincarnato commented 1 year ago

You cannot use the full matrix. SHAPEwarp will only use the probability of bases of being unpaired. You can pass these just like you do for SHAPE reactivities.