Abstract:
BACKGROUND: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.
journal_name
BMC Biotechnoljournal_title
BMC biotechnologyauthors
Zhou S,Ji G,Liu X,Li P,Moler J,Karro JE,Liang Cdoi
10.1186/1472-6750-12-16subject
Has Abstractpub_date
2012-05-03 00:00:00pages
16issn
1472-6750pii
1472-6750-12-16journal_volume
12pub_type
杂志文章abstract:BACKGROUND:Fungal laccases are multicopper oxidases with huge applicability in different sectors. Here, we describe the development of a set of high-throughput colorimetric assays for screening laccase libraries in directed evolution studies. RESULTS:Firstly, we designed three colorimetric assays based on the oxidatio...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-13-90
更新日期:2013-10-26 00:00:00
abstract:BACKGROUND:L-ornithine is effective in the treatment of liver diseases and helps strengthen the heart. The commercial applications mean that efficient biotechnological production of L-ornithine has become increasingly necessary. Adaptive evolution strategies have been proven a feasible and efficient technique to achiev...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-13-47
更新日期:2013-06-01 00:00:00
abstract:BACKGROUND:Each year, influenza is responsible for hundreds of thousand cases of illness and deaths worldwide. Due to the virus' fast mutation rate, the World Health Organization (WHO) is constantly on alert to rapidly respond to emerging pandemic strains. Although anti-viral therapies exist, the most proficient way to...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-015-0152-x
更新日期:2015-05-16 00:00:00
abstract:BACKGROUND:Quantum dots (QDs) have been considered as a new and efficient probe for labeling cells non-invasively in vitro and in vivo, but fairly little is known about how QDs are eliminated from cells after labeling. The purpose of this study is to investigate the metabolism of QDs in different type of cells. RESULT...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-10-36
更新日期:2010-05-06 00:00:00
abstract:BACKGROUND:Social amoeba, Dictyostelium discoideum, is a well-established model organism for studying cellular physiology and developmental pattern formation. Its haploid genome facilitates functional analysis of genes by a single round of mutagenesis including targeted disruption. Although the efficient generation of ...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-016-0267-8
更新日期:2016-04-14 00:00:00
abstract:BACKGROUND:Oleaginous yeast species are an alternative for the production of lipids or triacylglycerides (TAGs). These yeasts are usually non-pathogenic and able to store TAGs ranging from 20 % to 70 % of their cell mass depending on culture conditions. TAGs originating from oleaginous yeasts can be used as the so-call...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-016-0276-7
更新日期:2016-05-27 00:00:00
abstract:BACKGROUND:In the search for generic expression strategies for mammalian protein families several bacterial expression vectors were examined for their ability to promote high yields of soluble protein. Proteins studied included cell surface receptors (Ephrins and Eph receptors, CD44), kinases (EGFR-cytoplasmic domain, ...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-4-32
更新日期:2004-12-14 00:00:00
abstract:BACKGROUND:The CRISPR/Cas9 system is increasingly used for gene inactivation in mouse zygotes, but homology-directed mutagenesis and use of inbred embryos are less established. In particular, Rosa26 knock-in alleles for the insertion of transgenes in a genomic 'safe harbor' site, have not been produced. Here we applied...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-016-0234-4
更新日期:2016-01-16 00:00:00
abstract:: ...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-019-0504-z
更新日期:2019-02-18 00:00:00
abstract:BACKGROUND:Ultrasound and microbubbles (USMB) have been shown to enhance the intracellular uptake of molecules, generally thought to occur as a result of sonoporation. The underlying mechanism associated with USMB-enhanced intracellular uptake such as membrane disruption and endocytosis may also be associated with USMB...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-017-0364-3
更新日期:2017-05-18 00:00:00
abstract:BACKGROUND:Size exclusion chromatography is the method of choice for separating free from liposome-encapsulated molecules. However, if the column is not presaturated with lipids this type of chromatography causes a significant loss of lipid material. To date, the mechanism of lipid retention is poorly understood. It ha...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-5-11
更新日期:2005-05-10 00:00:00
abstract:BACKGROUND:As one of the genetic mechanisms for adaptive immunity, V(D)J recombination generates an enormous repertoire of T-cell receptors (TCRs). With the development of high-throughput sequencing techniques, systematic exploration of V(D)J recombination becomes possible. Multiplex PCR has been previously developed t...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-015-0153-9
更新日期:2015-05-28 00:00:00
abstract:BACKGROUND:CRISPR/Cas9 is widely used for precise genetic editing in various organisms. CRISPR/Cas9 editing may in many plants be hampered by the presence of complex and high ploidy genomes and inefficient or poorly controlled delivery of the CRISPR/Cas9 components to gamete cells or cells with regenerative potential. ...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-019-0530-x
更新日期:2019-06-17 00:00:00
abstract:BACKGROUND:The photorespiratory nitrogen cycle in C₃ plants involves an extensive diversion of carbon and nitrogen away from the direct pathways of assimilation. The liberated ammonia is re-assimilated, but up to 25% of the carbon may be released into the atmosphere as CO₂. Because of the loss of CO₂ and high energy co...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-11-111
更新日期:2011-11-21 00:00:00
abstract:BACKGROUND:Whole genome amplification (WGA) promises to eliminate practical molecular genetic analysis limitations associated with genomic DNA (gDNA) quantity. We evaluated the performance of multiple displacement amplification (MDA) WGA using gDNA extracted from lymphoblastoid cell lines (N = 27) with a range of start...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-5-24
更新日期:2005-09-16 00:00:00
abstract:BACKGROUND:Mesenchymal stem cells (MSCs) are of great interest in bone regenerative medicine due to their osteogenic potential and trophic effects. However, challenges to large-scale production of MSCs can hinder the translation of MSC therapies. 3D Microcarrier (MC)-based MSC culture presents a scalable and cost-effec...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-015-0219-8
更新日期:2015-10-31 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-9-29
更新日期:2009-03-31 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-017-0351-8
更新日期:2017-03-16 00:00:00
abstract:BACKGROUND:Waste animal fat is a promising feedstock to replace vegetable oil that widely used in commercial biodiesel process, however the high content of free fatty acid in waste fat makes it unfeasible to be processed with commercial base-catalytic process. Enzymatic process is preferable to convert waste fat into b...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-017-0390-1
更新日期:2017-09-09 00:00:00
abstract:BACKGROUND:The detection of unknown mutations is important in research and medicine. For this purpose, a mismatch-specific endonuclease CEL I from celery has been established as a useful tool in high throughput projects. Previously, CEL I-like activities were described only in a variety of plants and could not be expre...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-7-29
更新日期:2007-06-01 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
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更新日期:2021-01-13 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
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更新日期:2018-11-22 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-11-52
更新日期:2011-05-16 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-14-80
更新日期:2014-09-03 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/1472-6750-1-4
更新日期:2001-01-01 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
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更新日期:2015-01-31 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-018-0478-2
更新日期:2018-10-24 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-018-0486-2
更新日期:2018-12-12 00:00:00
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journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-019-0549-z
更新日期:2019-08-01 00:00:00
abstract:BACKGROUND:Serine hydroxymethyltransferase (SHMT) is the key enzyme in L-serine enzymatic production, suggesting the importance of obtaining a SHMT with high activity. RESULTS:Here, a novel SHMT gene, glyA, was obtained through degenerate oligonucleotide-primed PCR and encoded a novel SHMT with 54.3% similarity to the...
journal_title:BMC biotechnology
pub_type: 杂志文章
doi:10.1186/s12896-014-0093-9
更新日期:2014-11-14 00:00:00