Endogenous target mimic (eTMs) screen package
Based on the following rigorous rules:
(1) three unpaired nucleotides (bulges) are only permitted at the positions corresponding to the 9th to 12th nucleotides counting from the 5¡¯ end of a miRNA sequence;
(2) the 2nd to 8th positions at the 5¡¯ of a miRNA sequences must be perfectly pairing;
(3) the total number of mismatches and G/U pairs within the eTM and miRNA pairing region (excluding the bulge region) should be no more than three and the consecutive mismatches should not exceed two.
- Version update 0.2
- Add the screen of postive and negative chains together
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Demo:
run python eTMplant.py Arabidopsis_thaliana.fasta ath_miRNA.txt
Results will be in eTM_py_list.txt
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- Version update 0.3 (new command format)
- Add the parameter on penalty score (>=0).
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Demo:
run python eTMplant.py Arabidopsis_thaliana.fasta ath_miRNA.txt 4
Results (with penalty score <=4) will be in eTM_py_list.txt
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