Comparative EST Analyses in Plant Systems

Dong, Qunfeng; Kroiss, Lori; Oakley, Fredrick D.; Wang, Bingbing; Brendel, Volker

doi:10.1016/s0076-6879(05)95022-2

Cited by 22 publications

(4 citation statements)

References 46 publications

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“…The Kunitz-type scaffold is found not only in inhibitors of proteolytic enzymes but in toxins as well, for example in kalicludines. Some other polypeptides with antifungal and antimicrobial activities and those showing analgesic properties adopt the same scaffold [5,38,42,43]. In this group, the most represented sequences corresponded to the earlier described kalicludine-3 and to a new polypeptide kalicludine-4 (AsKC4).…”

Section: Resultsmentioning

confidence: 95%

The mining of toxin-like polypeptides from EST database by single residue distribution analysis

Kozlov

Grishin

2011

BMC Genomics

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BackgroundNovel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening.ResultsUsing the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined.ConclusionsThe suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

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Section: Resultsmentioning

confidence: 95%

The mining of toxin-like polypeptides from EST database by single residue distribution analysis

Kozlov

Grishin

2011

BMC Genomics

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“…An EST library, reflecting the cDNA in technical principle, only represents a very small proportion of genome sequences [27], [28] and is not specifically designed to capture miRNA precursor sequences. GSSs are nucleotide sequences similar to ESTs, with the exception that most are of origin from genome rather than miRNA.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, available dataset-based methods are in most case represented by EST+GSS[20], [23]–[26]. These sequences only represent a very small proportion of genome sequences [27], [28], and they are not specifically designed to include miRNA precursors. Thus, this strategy does not produce optimal results.…”

Section: Introductionmentioning

confidence: 99%

A Contig-Based Strategy for the Genome-Wide Discovery of MicroRNAs without Complete Genome Resources

et al. 2014

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MicroRNAs (miRNAs) are important regulators of many cellular processes and exist in a wide range of eukaryotes. High-throughput sequencing is a mainstream method of miRNA identification through which it is possible to obtain the complete small RNA profile of an organism. Currently, most approaches to miRNA identification rely on a reference genome for the prediction of hairpin structures. However, many species of economic and phylogenetic importance are non-model organisms without complete genome sequences, and this limits miRNA discovery. Here, to overcome this limitation, we have developed a contig-based miRNA identification strategy. We applied this method to a triploid species of edible banana (GCTCV-119, Musa spp. AAA group) and identified 180 pre-miRNAs and 314 mature miRNAs, which is three times more than those were predicted by the available dataset-based methods (represented by EST+GSS). Based on the recently published miRNA data set of Musa acuminate, the recall rate and precision of our strategy are estimated to be 70.6% and 92.2%, respectively, significantly better than those of EST+GSS-based strategy (10.2% and 50.0%, respectively). Our novel, efficient and cost-effective strategy facilitates the study of the functional and evolutionary role of miRNAs, as well as miRNA-based molecular breeding, in non-model species of economic or evolutionary interest.

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“…ESTs must be assembled into larger consensus sequences to be useful for phylogenetic purposes. This assembly is complicated computationally by alternative splicing and by gene duplication, both of which can generate ambiguous assemblies (Dong et al 2005). Moreover, the libraries are derived from the transcriptomes of specific tissues, and may be biased towards certain subsets of the genome.…”

Section: Genomicsmentioning

confidence: 99%

Construction and annotation of large phylogenetic trees

Sanderson¹

2007

Aust. Systematic Bot.

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Broad availability of molecular sequence data allows construction of phylogenetic trees with 1000s or even 10 000s of taxa. This paper reviews methodological, technological and empirical issues raised in phylogenetic inference at this scale. Numerous algorithmic and computational challenges have been identified surrounding the core problem of reconstructing large trees accurately from sequence data, but many other obstacles, both upstream and downstream of this step, are less well understood. Before phylogenetic analysis, data must be generated de novo or extracted from existing databases, compiled into blocks of homologous data with controlled properties, aligned, examined for the presence of gene duplications or other kinds of complicating factors, and finally, combined with other evidence via supermatrix or supertree approaches. After phylogenetic analysis, confidence assessments are usually reported, along with other kinds of annotations, such as clade names, or annotations requiring additional inference procedures, such as trait evolution or divergence time estimates. Prospects for partial automation of large-tree construction are also discussed, as well as risks associated with ‘outsourcing’ phylogenetic inference beyond the systematics community.

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Comparative EST Analyses in Plant Systems

Cited by 22 publications

References 46 publications

The mining of toxin-like polypeptides from EST database by single residue distribution analysis

The mining of toxin-like polypeptides from EST database by single residue distribution analysis

A Contig-Based Strategy for the Genome-Wide Discovery of MicroRNAs without Complete Genome Resources

Construction and annotation of large phylogenetic trees

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