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root/owl/trunk/src/owl/core/sequence
r1265
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alignment/ 1166 (10 years ago) by jmduarteg: Fixed bug: not allowing anymore the presence of gaps when choosing the representative CDS to uniprot match. Now the nucleotide alignments should be always correct (before they were shifted if there were gaps in CDS-to-uniprot)
geneticCode.dat 1114 (10 years ago) by jmduarteg: New feature: code for dna to protein translation
ReadingFrame.java 1114 (10 years ago) by jmduarteg: New feature: code for dna to protein translation
Sequence.java 1119 (10 years ago) by jmduarteg: Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
TranslationException.java 1119 (10 years ago) by jmduarteg: Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
Translator.java 1119 (10 years ago) by jmduarteg: Now checking also for ambiguous nucleotide codes (n, m) when translating. Changed implementation of translation by using the new Codon class.
GeneticCodeType.java 1132 (10 years ago) by jmduarteg: New SelectonRunner class. More taxonomy information retrieved from uniprot.
UniprotHomolog.java 1143 (10 years ago) by jmduarteg: New methods to check for reliability of positions with respect of the CDS matching
Codon.java 1154 (10 years ago) by jmduarteg: And all other amiguous codons
TranslatedFrame.java 1166 (10 years ago) by jmduarteg: Fixed bug: not allowing anymore the presence of gaps when choosing the representative CDS to uniprot match. Now the nucleotide alignments should be always correct (before they were shifted if there were gaps in CDS-to-uniprot)
ProteinToCDSMatch.java 1168 (10 years ago) by jmduarteg: Now catching the case when the best translation contains stop codons. This is usually due to a wrong genetic code, but for the moment it's still very difficult to know the genetic code from encoding organelle+organism taxonomy, so this is the temporary solution.
UniprotEntry.java 1172 (10 years ago) by jmduarteg: Now using apache commons logging
UniprotVerMisMatchException.java 1259 (10 years ago) by jmduarteg: New exception for mismatching uniprot versions
UniprotHomologList.java 1260 (10 years ago) by jmduarteg: Using the new UniprotVerMismatchException instead of IOException
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