d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences

Burke, John P.; Davison, Dan; Hide, Winston

doi:10.1101/gr.9.11.1135

Cited by 183 publications

(104 citation statements)

References 33 publications

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“…High-quality ESTs were first grouped into clusters by using the single-linkage clustering method (26). Two ESTs with Ͼ90% identity over Ͼ100-bp length were grouped into the same cluster.…”

Section: Methodsmentioning

confidence: 99%

The analysis of large-scale gene expression correlated to the phase changes of the migratory locust

Kang

Chen

Zhou

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

188

218

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The migratory locust is one of the most notorious agricultural pests that undergo a well known reversible, density-dependent phase transition from the solitary to the gregarious. To demonstrate the underlying molecular mechanisms of the phase change, we generated 76,012 ESTs from the whole body and dissected organs in the two phases. Comparing 12,161 unigene clusters, we identified 532 genes as phase-related (P < 0.01). Comprehensive assessment of the phase-related expression revealed that, whereas most of the genes in various categories from hind legs and the midgut are down-regulated in the gregarious phase, several gene classes in the head are impressively up-regulated, including those with peptidase, receptor, and oxygen-binding activities and those related to development, cell growth, and responses to external stimuli. Among them, a superfamily of proteins, the JHPH superfamily, which includes juvenile hormone-binding protein, hexamerins, prophenoloxidase, and hemocyanins, were highly expressed in the heads of the gregarious hoppers and hind legs of the solitary hoppers. Quantitative PCR experiments confirmed in part the EST results. These differentially regulated genes have strong functional implications that numerous molecular activities are involved in phase plasticity. This study provides ample molecular markers and genomic information on hemimetabolous insects and insights into the genetic and molecular mechanisms of phase changes in locusts.solitary phase ͉ gregarious phase ͉ EST ͉ unigene

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Section: Methodsmentioning

confidence: 99%

The analysis of large-scale gene expression correlated to the phase changes of the migratory locust

Kang

Chen

Zhou

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

188

218

View full text Add to dashboard Cite

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“…All 5Ј EST reads were treated with software PHRED (20,21) to remove vector sequences and low-quality regions, and then assembled into consensus sequences with software STACKPACK (version 2.1 patch 1) (22,23). The consensus sequences were used as ESTs to search against GenBank with the BLASTX program (24).…”

Section: Est Analysismentioning

confidence: 99%

Genes “Waiting” for Recruitment by the Adaptive Immune System: The Insights from Amphioxus

Yu¹,

Dong²,

Wu³

et al. 2005

The Journal of Immunology

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In seeking evidence of the existence of adaptive immune system (AIS) in ancient chordate, cDNA clones of six libraries from a protochordate, the Chinese amphioxus, were sequenced. Although the key molecules such as TCR, MHC, Ig, and RAG in AIS have not been identified from our database, we demonstrated in this study the extensive molecular evidence for the presence of genes homologous to many genes that are involved in AIS directly or indirectly, including some of which may represent the putative precursors of vertebrate AIS-related genes. The comparative analyses of these genes in different model organisms revealed the different fates of these genes during evolution. Their gene expression pattern suggested that the primitive digestive system is the pivotal place of the origin and evolution of the AIS. Our studies support the general statement that AIS appears after the jawless/jawed vertebrate split. However our study further reveals the fact that AIS is in its twilight in amphioxus and the evolution of the molecules in amphioxus are waiting for recruitment by the emergence of AIS.

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“…Here, we focus on computational methods, such as newly developed computer programs, because our experimental methods have been published previously (Carninci et al 1996(Carninci et al , 1997Sasaki et al 1998b;Seki et al 1998;Carninci and Hayashizaki 1999;Mizuno et al 1999). There have been many reports on the library assessments Salamov et al 1998) and clustering techniques (Boguski and Schuler 1995;Sutton et al 1995;Schuler et al 1996;Burke et al 1999;Miller et al 1999). Why did we develop new methods for old problems?…”

mentioning

confidence: 99%

“…Many clustering programs have been developed during the last few years. On a specialized computer, these programs can calculate the clustering of several million tag sequences in a few days (Boguski and Schuler 1995;Sutton et al 1995;Schuler et al 1996;Burke et al 1999;Miller et al 1999).…”

mentioning

confidence: 99%

Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library

Konno¹

2001

Genome Research

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We developed computer-based methods for constructing a nonredundant mouse full-length cDNA library. Our cDNA library construction process comprises assessment of library quality, sequencing the 3Ј ends of inserts and clustering, and completing a re-array to generate a nonredundant library from a redundant one. After the cDNA libraries are generated, we sequence the 5Ј ends of the inserts to check the quality of the library; then we determine the sequencing priority of each library. Selected libraries undergo large-scale sequencing of the 3Ј ends of the inserts and clustering of the tag sequences. After clustering, the nonredundant library is constructed from the original libraries, which have redundant clones. All libraries, plates, clones, sequences, and clusters are uniquely identified, and all information is saved in the database according to this identifier. At press time, our system has been in place for the past two years; we have clustered 939,725 3Ј end sequences into 127,385 groups from 227 cDNA libraries/sublibraries (see http://genome.gse.riken.go.jp/).[The sequence data described in this paper have been submitted to the DDBJ data library under accession nos. AV00011-AV175734, AV204013-AV382295, and BB561685-BB609425.]The collection of full-length genes requires libraries with a high content of full-length cDNA inserts, largescale sequencing, library assessment, and high-speed sequence clustering . Here, we focus on computational methods, such as newly developed computer programs, because our experimental methods have been published previously (Carninci et al.

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d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences

Cited by 183 publications

References 33 publications

The analysis of large-scale gene expression correlated to the phase changes of the migratory locust

The analysis of large-scale gene expression correlated to the phase changes of the migratory locust

Genes “Waiting” for Recruitment by the Adaptive Immune System: The Insights from Amphioxus

Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library

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