 ../
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alignment/
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1116
(12 years ago)
by jmduarteg:
Now properly translating all frames and finding the best translation match in checkEmblCDSMatching. New class doing all the matching of protein to CDS.
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UniprotEntry.java
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1137
(12 years ago)
by jmduarteg:
Now checking the sequence identity of the representative CDS to be above a minimum value.
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Codon.java
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1136
(12 years ago)
by jmduarteg:
New ambiguous nucleotide w.
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UniprotHomologList.java
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1133
(12 years ago)
by jmduarteg:
Fixed bug: getNucleotideAlignment was nullpointing when encountering a null return from getRepresentativeCDS() (which happens whenever there is no representative CDS for the particular UniprotEntry). Now checking for nulls before using the homolog in the alignment.
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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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ProteinToCDSMatch.java
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1126
(12 years ago)
by jmduarteg:
New code to obtain the nucleotide alignment by mapping the aminoacid alignment to the nucleotide sequences.
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TranslatedFrame.java
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1122
(12 years ago)
by jmduarteg:
Some refactoring
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UniprotHomolog.java
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1120
(12 years ago)
by jmduarteg:
New class UniprotEntry. Things make a lot more sense now...
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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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