Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.

By Bastien Chevreux, T. Pfisterer, B. Drescher, A. Driesel, W. Müller, T. Wetter, Sándor Suhai. Genome Research, 2004

1,070 citations recorded by the source corpus.

We present an EST sequence assembler that specializes in reconstruction of pristine mRNA transcripts, while at the same time detecting and classifying single nucleotide polymorphisms (SNPs) occuring in different variations thereof. The assembler uses iterative multipass strategies centered on high-confidence regions within sequences and has a fallback strategy for using low-confidence regions when needed. It features special functions to assemble high numbers of highly similar sequences without prior masking, an automatic editor that edits and analyzes alignments by inspecting the underlying traces, and detection and classification of sequence properties like SNPs with a high specificity and a sensitivity down to one mutation per sequence. In addition, it includes possibilities to use incorrectly preprocessed sequences, routines to make use of additional sequencing information such as base-error probabilities, template insert sizes, strain information, etc., and functions to detect and resolve possible misassemblies. The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b338f71e83763824b69f0afaec88e29d84359aa7

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Citations in the corpus

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. (2015, methodology): “The corrected sequences are highly accurate and can be assembled using a traditional OLC approach [48,53].”
Producing more with less: Strategies and novel technologies for plant-based food biofortification (2013, methodology): “As an example, sequencing and transcriptomic studies rely on tools such as MIRA (Chevreux et al., 2004), Myrna (Langmead, Hansen, & Leek, 2010), MG-RAST (Meyer et al.”
Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology (2011, neutral): “reference genome [38].”
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies (2015, methodology): “Tools such as Newbler (Roche), MIRA 4, 37 or AMOS, as well as the recent MetaAMOS, 38 are commonly used in metagenomics for performing referenced-based assemblies.”
A hitchhiker's guide to expressed sequence tag (EST) analysis (2006, methodology): “miraEST [50] can be used for the detection and classification of SNPs, by reconstructing mRNA transcripts from ESTs.”
Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1 (2010, neutral): “; Chevreux et al., 2004).”
SNP Discovery through Next-Generation Sequencing and Its Applications (2012, methodology): “Software programs such as Mira [73], SOAPdenovo [74], ABySS [75], and Velvet [76] have been used for de novo assembly.”
From RNA-seq reads to differential expression results (2010, methodology): “R-Se [97] TopHat [40] SplitSeek [36] De novo transcript assembler Oases [98] MIRA [99] Summarization Isoform-based Cufflinks [11] ALEXA-seq [10] Gene-based Count exons only For example, [34,45] Exon junction libraries [34,44]”
Elucidating modes of activation and herbicide resistance by sequence assembly and molecular modelling of the Acetolactate synthase complex in sugarcane. (2016, methodology): “…partial gene sequence and the sorghum EST assembly as templates, matching sequences were baited from the S. halepense short read dataset (accession: SRX142088) using the MIRABAIT component of the MIRA assembly software (version 4.9 beta) (Chevreux et al., 2004) and employing a k-mer size of 23.”
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons (2011, methodology): “Detecting these frameshifts with MACSE will help contiging the reads, with procedures like CAP3 [37] or miraEST [38], especially in low-coverage regions for which less sequencing information is available to choose among alternative base calls.”
The MaSuRCA genome assembler (2013, neutral): “4.0 (Chevreux et al., 2004), SOAPdenovo, SPAdes v2.”