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New EST Trimming Strategy
[chapter]
2005
Lecture Notes in Computer Science
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Trimming procedures are an important part of the sequence analysis pipeline in an EST Sequencing Project. ...
To remedy this drawback, we propose a new strategy, where each phase detects but does not remove its target, leaving this decision to a post processing step occurring after all phases. ...
The software phred has a parameter to turn on this trimming strategy. ...
doi:10.1007/11532323_24
fatcat:2v6ohandbbaj5kloqgzn4ikvpe
Trimming and clustering sugarcane ESTs
2001
Genetics and Molecular Biology
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In this paper the new trimming and clustering strategies are described in detail and we give the new official figures for the project, 237,954 expressed sequence tags and 43,141 clusters. ...
We therefore redesigned the clustering procedure entirely, including a much more careful initial trimming of the reads. ...
SUCEST data-users were pointing out many problems when we designed and implemented new trimming and clustering procedures. ...
doi:10.1590/s1415-47572001000100004
fatcat:k3sesbhax5dy7iufmntuntdcay
Expressed Sequence Tags With cDNA Termini: Previously Overlooked Resources for Gene Annotation and Transcriptome Exploration in Chlamydomonas reinhardtii
2008
Genetics
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impacts on downstream EST-based applications. ...
This work annotating differential ends of individual transcripts in the draft genome presents the research community with a new stream of data that will facilitate accurate determination of gene structures ...
We thank Erika Lindquist from JGI who makes their final EST sequences available for public download. ...
doi:10.1534/genetics.107.085605
pmid:18493042
pmcid:PMC2390652
fatcat:46f2yv3ukjf3zlsn7r4eyjgeae
An optimized procedure greatly improves EST vector contamination removal
2007
BMC Genomics
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number of errors remained after preliminary trimming. ...
The modified trimming procedure for SeqClean was also compared with the trimming efficiency of the other two popular programs, LUCY2, and cross_match. ...
In that case, an alternative sampling strategy should be considered. ...
doi:10.1186/1471-2164-8-416
pmid:17997864
pmcid:PMC2194723
fatcat:pg7oshakzvca3nwbwcrpyebxju
De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data
2009
Genome Biology
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Abbreviations EST: expressed sequence tag; GA: Genome Analyzer; Gc: Grosmannia clavigera; indel: insertion or deletion; NCBI: National Center for Biotechnology Information; PE: pairedend; QRL: quality ...
We quantified the efficiency of discovering new and useful sequence data, as well as the rate at which the new sequence data covered GCgb1. ...
Because the 454 assemblies also had acceptably low EST-detectable misassembly rates, we concluded that a strategy that combined all three read types would be optimal. ...
doi:10.1186/gb-2009-10-9-r94
pmid:19747388
pmcid:PMC2768983
fatcat:xmpfhd2zircz3dobigyz4kuaoy
Bioinformatics for the Citrus EST Project (CitEST)
2007
Genetics and Molecular Biology
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mansoni EST (Verjovski-Almeida et al., 2003) , CitEST has its own improvements, and some new tools developed by the CBL team. ...
Introduction With more than 300,000 clones sequenced, the Citrus EST Project (CitEST) is a large transcriptome sequencing project, and has the purpose of integrating knowledge on genetic mapping with new ...
doi:10.1590/s1415-47572007000500031
fatcat:d5ouhy67kvbjpcnhs4kgiqa6ve
A Novel Terminal-Repeat Retrotransposon in Miniature (TRIM) Is Massively Expressed inEchinococcus multilocularisStem Cells
2015
Genome Biology and Evolution
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ta-TRIM (taeniid TRIM). ta-TRIMs are only the second family of TRIM elements discovered in animals, and are likely the result of convergent reductive evolution in different taxonomic groups. ...
Future studies of active and inactive ta-TRIM elements could give the first clues on MGE silencing mechanisms in cestodes. ...
Expression of ta-TRIM Elements and the Generation of New Transcripts The EST evidence suggests that in all the analyzed taeniid species, ta-TRIMs are transcribed at very high levels (>1% of all polyadenylated ...
doi:10.1093/gbe/evv126
pmid:26133390
pmcid:PMC4558846
fatcat:rb64jsubpba2tdk52e2n3jdc54
Analysis of slipped sequences in EST projects
2006
Genetics and Molecular Research
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The subsequence strategy is better than the suffix strategy, because it is not anchored at the end of the sequence, so it is more flexible to find slippage at the beginning of the EST. ...
We propose three new methods to detect slippage artifacts: arithmetic mean method, geometric mean method, and echo coverage method. ...
Thus, sequence trimming is an important step that must be performed in EST sequencing projects. Slippage is an artifact type that can be found in EST sequences. ...
pmid:16755508
fatcat:e2y3zyylbvblpp4dppi7hyge6q
Page 85 of Genetics Vol. 179, Issue 1
[page]
2008
Genetics
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We adopted the new version of Phred (040406.c) (EWING ef al. 1998; B. ...
To evaluate the potential impact of incorrectly trimmed ESTs on downstream applications, we scanned all EST contig (consensus) sequences for complete, partial, and or abnormal termini.
tively; 5TNS and ...
La réponse interféron
La réponse interféron - Un grand pouvoir implique de grandes responsabilités
2020
M S.Médecine Sciences
La réponse interféron - Un grand pouvoir implique de grandes responsabilités
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IRF7-P est également un substrat de Pin1. ...
Ces protéines partagent une organisation tripartite, à l'origine de leur nom, constituée d'un domaine RING (really interesting new gene), d'un ou deux domaines B-box, et d'un domaine coiled-coil. ...
doi:10.1051/medsci/2020032
pmid:32228834
fatcat:xq27eve3dndgbcb6pkybanitlm
cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome
2007
BMC Genomics
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Assembly of our sequence tags produced 2548 contigs and 2671 singletons versus 5220 contigs and 5910 singletons when our EST were assembled with EST in public databases. ...
Comparison of all the assembled EST/contigs with predicted CDS and genomic sequences in the PlasmoDB database identified 356 genes with predicted coding sequences fully covered by EST, including 85 genes ...
More efforts with new strategies will be required for obtaining full cDNA sequences for the large genes. ...
doi:10.1186/1471-2164-8-255
pmid:17662120
pmcid:PMC1978503
fatcat:byhad6mwkvgq3mbuiqjkcxnkhy
Comparing de novo assemblers for 454 transcriptome data
2010
BMC Genomics
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Combining differently optimal assemblies from different programs however gave a more credible final product, and this strategy is recommended. ...
We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode ...
The longest unmasked portion of the sequence was used to set new trim points in the SFF file. ...
doi:10.1186/1471-2164-11-571
pmid:20950480
pmcid:PMC3091720
fatcat:swq6ez7f3vd5ddsfop7pjnvhqq
Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes
2001
Proceedings of the National Academy of Sciences of the United States of America
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A new group of long terminal repeats (LTR) retrotransposons, termed terminal-repeat retrotransposons in miniature (TRIM), are described that are present in both monocotyledonous and dicotyledonous plant ...
In solanaceous species and maize, TRIM elements provided target sites for further retrotransposon insertions. ...
‡ Each EST represents a TRIM insertion in a different gene (duplicate ESTs for
the same gene were not counted). ...
doi:10.1073/pnas.241341898
pmid:11717436
pmcid:PMC61118
fatcat:edpj7u6yljhf5oxuu6yrduimoi
OrchidBase: A Collection of Sequences of the Transcriptome Derived from Orchids
2011
Plant and Cell Physiology
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The OrchidBase database is freely available at http://lab.fhes.tn .edu.tw/est. ...
Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-generation sequencing (NGS) including both Roche 454 and ...
After confirming EST quality with 'Low Quality Sequences Trimming' and having trimmed the vector sequence to obtain high-quality sequence, EST sequences were clustered and assembled into contigs and singletons ...
doi:10.1093/pcp/pcq201
pmid:21245031
fatcat:22k25zmtu5envdyk4phhpekkai
Robust statistical methods in R using the WRS2 package
2019
Behavior Research Methods
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Least squares regression inherits all of these concerns and new concerns are introduced. A strategy for salvaging classic methods is to test assumptions. ...
One-way test medians (med1way): It follows the same testing strategy as the one for the trimmed means. ...
, and h 1 and h 2 the number of observations left after trimming. ...
doi:10.3758/s13428-019-01246-w
pmid:31152384
fatcat:77eudnmal5gupcx724yv6xmjsi
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