Splicing graphs and EST assembly problem

Heber, Steffen; Alekseyev, Max A.; Sze, Sing‐Hoi; Tang, Haixu; Pevzner, Pavel A.

doi:10.1093/bioinformatics/18.suppl_1.s181

Cited by 190 publications

(162 citation statements)

References 23 publications

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“…Indeed, as discussed later in more detail, 50.4% of the 3Ј reads gave no BLASTx hit, whereas 27.7% of the 5Ј reads gave no hit. As the project continued, we increased the percentage of 3Ј reads to facilitate the clustering and assembly of ESTs into contigs (Heber et al, 2002;Wang et al, 2004).…”

Section: Characterization Of the Total Est Collectionmentioning

confidence: 99%

cDNA Sequences for Transcription Factors and Signaling Proteins of the HemichordateSaccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism

Freeman

et al. 2008

The Biological Bulletin

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Abstract.We describe a collection of expressed sequence tags (ESTs) for Saccoglossus kowalevskii, a directdeveloping hemichordate valuable for evolutionary comparisons with chordates. The 202,175 ESTs represent 163,633 arrayed clones carrying cDNAs prepared from embryonic libraries, and they assemble into 13,677 continuous sequences (contigs), leaving 10,896 singletons (excluding mitochondrial sequences). Of the contigs, 53% had significant matches when BLAST was used to query the NCBI databases (Յ10 Ϫ10 ), as did 51% of the singletons. Contigs most frequently matched sequences from amphioxus (29%), chordates (67%), and deuterostomes (87%). From the clone array, we isolated 400 full-length sequences for transcription factors and signaling proteins of use for evolutionary and developmental studies. The set includes sequences for fox, pax, tbx, hox, and other homeobox-containing factors, and for ligands and receptors of the TGF␤, Wnt, Hh, Delta/ Notch, and RTK pathways. At least 80% of key sequences have been obtained, when judged against gene lists of model organisms. The median length of these cDNAs is 2.3 kb, including 1.05 kb of 3Ј untranslated region (UTR). Only 30% are entirely matched by single contigs assembled from ESTs. We conclude that an EST collection based on 150,000 clones is a rich source of sequences for molecular developmental work, and that the EST approach is an efficient way to initiate comparative studies of a new organism.

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Section: Characterization Of the Total Est Collectionmentioning

confidence: 99%

cDNA Sequences for Transcription Factors and Signaling Proteins of the HemichordateSaccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism

Freeman

et al. 2008

The Biological Bulletin

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“…Capturing the 59R39 directionality of transcription, they naturally all form directed acyclic graphs (DAGs). Going back to [33], matching (parts of) ESTs [22,34,35] have been used as nodes connected by edges representing the EST evidence, in order to cluster them and/or to allow the analysis of AS. Heber and co-workers [35] subsequently collapse (remove) vertices with indegree (i.e., the number of inedges) = outdegree (the number of outedges) = 1.…”

Section: Introductionmentioning

confidence: 99%

“…Going back to [33], matching (parts of) ESTs [22,34,35] have been used as nodes connected by edges representing the EST evidence, in order to cluster them and/or to allow the analysis of AS. Heber and co-workers [35] subsequently collapse (remove) vertices with indegree (i.e., the number of inedges) = outdegree (the number of outedges) = 1. Later on, two works from the same year proposed a graph structure where every vertex corresponds to a splice site and the connecting edges represent the intermediate exon/intron [36,37], labelled according to the mRNA or EST evidence.…”

Section: Introductionmentioning

confidence: 99%

A General Definition and Nomenclature for Alternative Splicing Events

Sammeth¹,

Foissac²,

Guigó³

2008

SciVee

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Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) is a key phenomenon contributing to the production of different mature transcripts from the same primary RNA sequence. As a plethora of different transcript forms is available in databases, a first step to uncover the biology that drives AS is to identify the different types of reflected splicing variation. In this work, we present a general definition of the AS event along with a notation system that involves the relative positions of the splice sites. This nomenclature univocally and dynamically assigns a specific ''AS code'' to every possible pattern of splicing variation. On the basis of this definition and the corresponding codes, we have developed a computational tool (AStalavista) that automatically characterizes the complete landscape of AS events in a given transcript annotation of a genome, thus providing a platform to investigate the transcriptome diversity across genes, chromosomes, and species. Our analysis reveals that a substantial part-in human more than a quarter-of the observed splicing variations are ignored in common classification pipelines. We have used AStalavista to investigate and to compare the AS landscape of different reference annotation sets in human and in other metazoan species and found that proportions of AS events change substantially depending on the annotation protocol, species-specific attributes, and coding constraints acting on the transcripts. The AStalavista system therefore provides a general framework to conduct specific studies investigating the occurrence, impact, and regulation of AS.

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“…Instead of a comprehensive review, we will just name a few results below. To enumerate all possible isoforms, a core ingredient is the splicing graph (Heber et al, 2002;Sammeth et al, 2008a). A predetermined parameter ''dimension'' decides how many transcripts are compared simultaneously.…”

Section: Introductionmentioning

confidence: 99%

Inference of Isoforms from Short Sequence Reads

Feng

Jiang

2010

Lecture Notes in Computer Science

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Due to alternative splicing events in eukaryotic species, the identification of mRNA isoforms (or splicing variants) is a difficult problem. Traditional experimental methods for this purpose are time consuming and cost ineffective. The emerging RNA-Seq technology provides a possible effective method to address this problem. Although the advantages of RNASeq over traditional methods in transcriptome analysis have been confirmed by many studies, the inference of isoforms from millions of short sequence reads (e.g., Illumina/Solexa reads) has remained computationally challenging. In this work, we propose a method to calculate the expression levels of isoforms and infer isoforms from short RNA-Seq reads using exon-intron boundary, transcription start site (TSS) and poly-A site (PAS) information. We first formulate the relationship among exons, isoforms, and single-end reads as a convex quadratic program, and then use an efficient algorithm (called IsoInfer) to search for isoforms. IsoInfer can calculate the expression levels of isoforms accurately if all the isoforms are known and infer novel isoforms from scratch. Our experimental tests on known mouse isoforms with both simulated expression levels and reads demonstrate that IsoInfer is able to calculate the expression levels of isoforms with an accuracy comparable to the stateof-the-art statistical method and a 60 times faster speed. Moreover, our tests on both simulated and real reads show that it achieves a good precision and sensitivity in inferring isoforms when given accurate exon-intron boundary, TSS, and PAS information, especially for isoforms whose expression levels are significantly high. The software is publicly available for free at

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Splicing graphs and EST assembly problem

Cited by 190 publications

References 23 publications

cDNA Sequences for Transcription Factors and Signaling Proteins of the HemichordateSaccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism

cDNA Sequences for Transcription Factors and Signaling Proteins of the HemichordateSaccoglossus kowalevskii: Efficacy of the Expressed Sequence Tag (EST) Approach for Evolutionary and Developmental Studies of a New Organism

A General Definition and Nomenclature for Alternative Splicing Events

Inference of Isoforms from Short Sequence Reads

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