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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"o.b.n.core.sequence.CDSSequence doesn't reverse-complement correctly","articleBody":"Given a transcript sequence derived from a GeneSequence defined on reverse strand of a chromosomal sequence, the method getCodingSequence doesn't return the reverse complement, but just the reverse.\r\n\r\nThis seems to be due to the complement being made twice:\r\n\r\n```java\r\nString sequence = this.getSequenceAsString(getBioBegin(), getBioEnd(), getStrand()); \r\n```\r\nin CDSSequence# getCodingSequence() \r\n\r\ngenerates the reverse complement, but subsequent code makes a complementary sequence again, so the end result is simply a reversed sequence.\r\n\r\nA simple fix might be just to remove this second complementation, but possibly it might be needed in some circumstances.\r\n\r\nThe bug is exposed by test TranscriptSequenceTest#getCDNASeqNegativeStrand() \r\n\r\n","author":{"url":"https://github.com/richarda23","@type":"Person","name":"richarda23"},"datePublished":"2022-01-04T18:11:50.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":0},"url":"https://github.com/1016/biojava/issues/1016"}