 ../
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alignment/
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1166
(11 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)
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UniprotEntry.java
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1172
(11 years ago)
by jmduarteg:
Now using apache commons logging
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UniprotHomologList.java
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1172
(11 years ago)
by jmduarteg:
Now using apache commons logging
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ProteinToCDSMatch.java
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1168
(11 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.
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TranslatedFrame.java
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1166
(11 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)
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Codon.java
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1154
(12 years ago)
by jmduarteg:
And all other amiguous codons
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UniprotHomolog.java
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1143
(12 years ago)
by jmduarteg:
New methods to check for reliability of positions with respect of the CDS matching
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GeneticCodeType.java
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1132
(12 years ago)
by jmduarteg:
New SelectonRunner class. More taxonomy information retrieved from uniprot.
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Sequence.java
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1119
(12 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.
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TranslationException.java
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1119
(12 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.
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Translator.java
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1119
(12 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.
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geneticCode.dat
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1114
(12 years ago)
by jmduarteg:
New feature: code for dna to protein translation
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ReadingFrame.java
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1114
(12 years ago)
by jmduarteg:
New feature: code for dna to protein translation
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