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dc.contributor.authorZhou, Sun
dc.contributor.authorJi, Guoli
dc.contributor.author吉国力
dc.contributor.authorLiu, Xiaolin
dc.contributor.authorLi, Pei
dc.contributor.authorMoler, James
dc.contributor.authorKarro, John E.
dc.contributor.authorLiang, Chun
dc.date.accessioned2013-04-03T03:32:20Z
dc.date.available2013-04-03T03:32:20Z
dc.date.issued2012-05-03
dc.identifier.citationBMC BIOTECHNOLOGY,2012,12zh_CN
dc.identifier.issn1472-6750
dc.identifier.urihttp://dx.doi.org/10.1186/1472-6750-12-16
dc.identifier.uriWOS:000307756400001
dc.identifier.urihttps://dspace.xmu.edu.cn/handle/2288/15472
dc.description.abstractBackground: Expressed Sequence Tag (EST) sequences are widely used in applications such as genome annotation, gene discovery and gene expression studies. However, some of GenBank dbEST sequences have proven to be "unclean". Identification of cDNA termini/ends and their structures in raw ESTs not only facilitates data quality control and accurate delineation of transcription ends, but also furthers our understanding of the potential sources of data abnormalities/errors present in the wet-lab procedures for cDNA library construction. Results: After analyzing a total of 309,976 raw Pinus taeda ESTs, we uncovered many distinct variations of cDNA termini, some of which prove to be good indicators of wet-lab artifacts, and characterized each raw EST by its cDNA terminus structure patterns. In contrast to the expected patterns, many ESTs displayed complex and/or abnormal patterns that represent potential wet-lab errors such as: a failure of one or both of the restriction enzymes to cut the plasmid vector; a failure of the restriction enzymes to cut the vector at the correct positions; the insertion of two cDNA inserts into a single vector; the insertion of multiple and/or concatenated adapters/linkers; the presence of 3'-end terminal structures in designated 5'-end sequences or vice versa; and so on. With a close examination of these artifacts, many problematic ESTs that have been deposited into public databases by conventional bioinformatics pipelines or tools could be cleaned or filtered by our methodology. We developed a software tool for Abnormality Filtering and Sequence Trimming for ESTs (AFST, http://code.google.com/p/afst/) using a pattern analysis approach. To compare AFST with other pipelines that submitted ESTs into dbEST, we reprocessed 230,783 Pinus taeda and 38,709 Arachis hypogaea GenBank ESTs. We found 7.4% of Pinus taeda and 29.2% of Arachis hypogaea GenBank ESTs are "unclean" or abnormal, all of which could be cleaned or filtered by AFST. Conclusions: cDNA terminal pattern analysis, as implemented in the AFST software tool, can be utilized to reveal wet-lab errors such as restriction enzyme cutting abnormities and chimeric EST sequences, detect various data abnormalities embedded in existing Sanger EST datasets, improve the accuracy of identifying and extracting bona fide cDNA inserts from raw ESTs, and therefore greatly benefit downstream EST-based applications.zh_CN
dc.description.sponsorshipNational Natural Science Foundation of China [61174161]; Specialized Research Fund for the Doctoral Program of Higher Education of China [20090121110022]; Xiamen University [2011121047, 201112 G018, CXB2011035, 0630-E72000]; Key Research Project of Fujian Province of China [2009H0044]zh_CN
dc.language.isoenzh_CN
dc.publisherBIOMED CENTRAL LTDzh_CN
dc.subjectcDNA terminuszh_CN
dc.subjectcDNA library constructionzh_CN
dc.subjectPattern analysiszh_CN
dc.subjectRestriction enzyme cutting abnormalityzh_CN
dc.subjectChimeric EST sequenceszh_CN
dc.titlePattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST datazh_CN
dc.typeArticlezh_CN


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