“Chimera (EST)”的意思、由来-开放百科全书

In genetics and molecular biology, a chimera is a single DNA sequence originating from multiple transcripts or parent sequences. It can occur in various contexts. Chimeras are generally considered a contaminant, as a chimera can be interpreted as a novel sequence while it is in fact an artifact. However, the formation of artificial chimeras can also be a useful tool in the molecular biology. For example, in protein engineering, "chimeragenesis (forming chimeras between proteins that are encoded by homologous cDNAs)"^[1] is one of the "two major techniques used to manipulate cDNA sequences".^[1]

Transcript chimera

A chimera can occur as a single cDNA sequence originating from two transcripts. It is usually considered to be a contaminant in transcript and expressed sequence tag (EST) databases.^[2] It is estimated that approximately 1% of all transcripts in the National Center for Biotechnology Information's Unigene database contain a "chimeric sequence".^[3]

PCR chimera

A chimera can also be an artifact of PCR amplification. It occurs when the extension of an amplicon is aborted, and the aborted product functions as a primer in the next PCR cycle. The aborted product anneals to the wrong template and continues to extend, thereby synthesizing a single sequence sourced from two different templates^[4].

PCR chimeras are an important issue to take into account during metabarcoding, where DNA sequences from environmental samples are used to determine biodiversity. A chimera is a novel sequence that will most probably not match to any known organism. Hence, it might be interpreted as a new species thereby inflating over diversity.

Chimeric read

A chimeric read is a digital DNA sequence (i.e. a string of letters in a file that can be read as a DNA sequence) that originates from an actual chimera (i.e. an physical DNA sequence in a sample) or produced due to misreading the sample. The latter is known to occur with sequencing of electrophoresis gels^[5].

Examples

See also

References

1. ^¹{{Cite book|title=Handbook of Neurochemistry and Molecular Neurobiology Neural Membranes and Transport|author1=Lajtha, Abel|author2=E. A. Reith, Maarten|publisher=Springer Science+Business Media, LLC.|year=2007|isbn=978-0-387-30347-5|location=Boston, MA|pages=485}} p. 424
2. ^{{cite journal | last1 = Unneberg | first1 = P | last2 = Claverie | first2 = JM | last3 = Hoheisel | first3 = Jörg | title = Tentative Mapping of Transcription-Induced Interchromosomal Interaction using Chimeric EST and mRNA Data | journal = PLoS ONE | volume = 2 | issue = 2 | pages = e254 | year = 2007 | pmid = 17330142 | pmc = 1804257 | doi = 10.1371/journal.pone.0000254 | editor1-last = Hoheisel | editor1-first = Jörg | bibcode = 2007PLoSO...2..254U }} {{open access}}
3. ^{{cite web |url=http://www.chem.agilent.com/Library/applications/5989_0750_EST_final72.pdf |title=EST Assembly for the Creation of Oligonucleotide Probe Targets |author=Charlie Nelson |publisher=Agilent Technologies |accessdate=May 12, 2009}}
4. ^{{Cite journal|last=Birren|first=Bruce W.|last2=Knight|first2=Rob|last3=Petrosino|first3=Joseph F.|last4=Consortium|first4=The Human Microbiome|last5=DeSantis|first5=Todd Z.|last6=Methé|first6=Barbara|last7=Sodergren|first7=Erica|last8=Highlander|first8=Sarah K.|last9=Tabbaa|first9=Diana|date=2011-03-01|title=Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons|url=http://genome.cshlp.org/content/21/3/494|journal=Genome Research|language=en|volume=21|issue=3|pages=494–504|doi=10.1101/gr.112730.110|issn=1549-5469|pmc=3044863|pmid=21212162}}
5. ^{{Cite web|url=https://scienceblogs.com/digitalbio/2007/02/01/sequencing-a-genome-part-vi-ch|title=Sequencing a Genome, part VI: Chimeras are not just funny-looking animals {{!}} ScienceBlogs|website=scienceblogs.com|access-date=2019-01-10}}
6. ^{{cite journal|last1=Maidak|first1=B.|year=1996|title=The Ribosomal Database Project (RDP)|url=http://nar.oxfordjournals.org/cgi/content/full/24/1/82#tbl01|journal=Nucleic Acids Research|volume=24|issue=1|pages=82–85|doi=10.1093/nar/24.1.82|accessdate=May 12, 2009}}
7. ^{{Cite web|url=http://qiime.org/tutorials/chimera_checking.html|title=Chimera checking sequences with QIIME — Homepage|website=qiime.org|access-date=2019-01-10}}
8. ^{{Cite journal|last=Birren|first=Bruce W.|last2=Knight|first2=Rob|last3=Petrosino|first3=Joseph F.|last4=Consortium|first4=The Human Microbiome|last5=DeSantis|first5=Todd Z.|last6=Methé|first6=Barbara|last7=Sodergren|first7=Erica|last8=Highlander|first8=Sarah K.|last9=Tabbaa|first9=Diana|date=2011-03-01|title=Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons|url=http://genome.cshlp.org/content/21/3/494|journal=Genome Research|language=en|volume=21|issue=3|pages=494–504|doi=10.1101/gr.112730.110|issn=1549-5469|pmc=3044863|pmid=21212162}}
9. ^{{Cite web|url=http://drive5.com/usearch/manual/uchime_algo.html|title=UCHIME algorithm|website=drive5.com|access-date=2019-01-10}}
10. ^{{Cite web|url=https://www.rdocumentation.org/packages/dada2/versions/1.0.3/topics/removeBimeraDenovo|title=removeBimeraDenovo function {{!}} R Documentation|website=www.rdocumentation.org|access-date=2019-01-10}}
11. ^{{Cite journal|last=Hugenholtz|first=Philip|last2=Faulkner|first2=Geoffrey|last3=Huber|first3=Thomas|date=2004-09-22|title=Bellerophon: a program to detect chimeric sequences in multiple sequence alignments|url=https://academic.oup.com/bioinformatics/article/20/14/2317/213951|journal=Bioinformatics|language=en|volume=20|issue=14|pages=2317–2319|doi=10.1093/bioinformatics/bth226|pmid=15073015|issn=1367-4803}}
12. ^{{cite web | title=Entrez Gene: CYP2C18 cytochrome P450, family 2, subfamily C, polypeptide 18| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=1562 |publisher=National Center for Biotechnology Information |accessdate=May 12, 2009}}