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I understand that chimeric sequence identification is done in results of sequencing projects to remove them and improve the quality of the output. I am unsure as to how they show up during sequencing. Any explanation is appreciated.

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closed as unclear what you're asking by leonardo, Chris, terdon, Cornelius, fileunderwater May 11 at 19:37

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Do you mean chimeric sequences that are artifacts of the sequencing process or actual bona fide chimeric transcripts that are present in vivo? –  terdon Apr 26 at 11:32
    
Chimeric sequences in the sequencing process.. I mentioned that in the first line.. –  The Last Word Apr 27 at 5:14
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Yes, but you're contradicting yourself. Some chimeric sequences are very real and exist in vivo. Others are artifacts, mistakes introduced by the sequencing process. Which ones are you asking about? –  terdon May 11 at 15:12
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Chimeric sequences show up in sequencing projects a lot and you always have to watch for them. They show up a lot for a couple of reasons.

Firstly, sequencers are not perfect and generate sequences with errors. Also they produce a lot of data but often not quite enough. There are usually thin spots in the sequence assembly - regions which are not covered very well.

When a sequencing error coincides with a gap in the sequencing, the two ends of a sequence alignment can align to two unrelated or distant segments of sequence, creating an alignment assembly which has two unrelated portions - a chimera.

This is especially the case in EST and RnaSeq runs where long scaffold sequences and higher coverage might not help as much. It does have an impact in Chromosomal sequencing as well. There's some interest in how often contaminating DNA get included into sequencing output.

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My understanding of chimeric sequences is that they are produced as the result of inserting two different cDNAs (usually from different species) into a backbone such as pUAST to make a protein that is partly from one species and partly from another species. Sometimes you want to do this because for example the ligand for a receptor in lets say Drosophila is very difficult to produce but the ligand for the mammalian receptor is easily available so what scientists do is that they attach the human cDNA corresponding to the extracellular side of the receptor to the Drosophila intercellular portion of the Drosophila receptor. Now you can intracellularly activate a Drosophila receptor using a human ligand for a receptor. Now I have never seen/heard of chimeric in vivo sequences and that just doesn't seem possible but what I imagine can happen when viewing sequencing data for a species that are not fully sequences is that the search engines says a particular sequence is from a different species that you have sequenced. This is because the database will try to find the closest match to the sequence. NCBI BLAST for example can do this but usually it gives you a percentage sequence matching/probability. Otherwise I'm not sure what you mean by the word sequencing projects. Could you provide an example/reference?

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