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New EST Trimming Strategy [chapter]

Christian Baudet, Zanoni Dias
2005 Lecture Notes in Computer Science  
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

Guilherme P. Telles, Felipe R. da Silva
2001 Genetics and Molecular Biology  
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

C. Liang, Y. Liu, L. Liu, A. C. Davis, Y. Shen, Q. Q. Li
2008 Genetics  
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

Yi-An Chen, Chang-Chun Lin, Chin-Di Wang, Huan-Bin Wu, Pei-Ing Hwang
2007 BMC Genomics  
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

Scott DiGuistini, Nancy Y Liao, Darren Platt, Gordon Robertson, Michael Seidel, Simon K Chan, T Roderick Docking, Inanc Birol, Robert A Holt, Martin Hirst, Elaine Mardis, Marco A Marra (+4 others)
2009 Genome Biology  
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)

Marcelo S. Reis, Marco A. Takita, Darío A. Palmieri, Marcos A. Machado
2007 Genetics and Molecular Biology  
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

Uriel Koziol, Santiago Radio, Pablo Smircich, Magdalena Zarowiecki, Cecilia Fernández, Klaus Brehm
2015 Genome Biology and Evolution  
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

Christian Baudet, Zanoni Dias
2006 Genetics and Molecular Research  
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  
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

Ghizlane Maarifi, Nikaïa Smith, Sébastien Nisole
2020 M S.Médecine Sciences  
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

Fangli Lu, Hongying Jiang, Jinhui Ding, Jianbing Mu, Jesus G Valenzuela, José MC Ribeiro, Xin-zhuan Su
2007 BMC Genomics  
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

Sujai Kumar, Mark L Blaxter
2010 BMC Genomics  
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

C.-P. Witte, Q. H. Le, T. Bureau, A. Kumar
2001 Proceedings of the National Academy of Sciences of the United States of America  
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

C.-H. Fu, Y.-W. Chen, Y.-Y. Hsiao, Z.-J. Pan, Z.-J. Liu, Y.-M. Huang, W.-C. Tsai, H.-H. Chen
2011 Plant and Cell Physiology  
The OrchidBase database is freely available at  ...  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

Patrick Mair, Rand Wilcox
2019 Behavior Research Methods  
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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