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Last change
on this file was
5390,
checked in by westram, 18 years ago
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-
Property svn:eol-style set to
native
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Property svn:keywords set to
Author Date Id Revision
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File size:
1.6 KB
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| 1 | Count nucleotides, nuc#|sequence|count("agctuAGCTU") |
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| 2 | Count nucleotides (incl. IUPAC), nuc#|sequence|count("agctumrwsykvhdbnAGCTUMRWSYKVHDBN") |
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| 3 | Count nucleotides gene, nuc_term#|sequence|filter(SAI=termini,include=x)|count("ACGTU") |
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| 4 | Count amino acids, aa#|sequence|count("ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy") |
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| 5 | Count poison characters (RNA/DNA), poison#|sequence|len;count("acgtumrwsykvhdbnACGTUMRWSYKVHDBN-.")|minus |
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| 6 | Count poison characters (PRO), poison#|sequence|len;count("abcdefghiklmnpqrstvwxyzABCDEFGHIKLMNPQRSTVWXYZ-.*")|minus |
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| 7 | Replace poison characters with gaps (RNA/DNA), |translate("acgtumrwsykvhdbnACGTUMRWSYKVHDBN-.","acgtumrwsykvhdbnACGTUMRWSYKVHDBN-.","-") |
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| 8 | Replace poison characters with gaps (PRO), |translate("abcdefghiklmnpqrstvwxyzABCDEFGHIKLMNPQRSTVWXYZ-.*","abcdefghiklmnpqrstvwxyzABCDEFGHIKLMNPQRSTVWXYZ-.*","-") |
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| 9 | start gene, start#|sequence|filter(SAI=5_prime,exclude=x)|count("ACGTUMRWSYKVHDBNacgtumrwsykvhdbn") |
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| 10 | end gene, end#|sequence|filter(SAI=3_prime,exclude=x)|count("ACGTUMRWSYKVHDBNacgtumrwsykvhdbn") |
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| 11 | calculate G+C content, GC#|sequence|count("gcGC");count("agctuAGCTU")|"G+C:";per_cent |
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| 12 | calculate G+C content helical parts only, GCH#|sequence|filter(SAI=HELIX;exclude=.-)|count("gcGC");count("agctuAGCTU")|"GCH=";per_cent;"(";cut(2);")" |
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| 13 | calculate G+C content non helical parts only, GCN#|sequence|filter(SAI=HELIX;include=.-)|count("gcGC");count("agctuAGCTU")|"GCN=";per_cent;"(";cut(2);")" |
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| 14 | |
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