Alternative Parallelization Strategies in EST Clustering

Trivedi, Nishank; Pedretti, Kevin; Braun, Terry A.; Scheetz, Todd E.; Casavant, Thomas L.

doi:10.1007/978-3-540-45145-7_36

Cited by 8 publications

(4 citation statements)

References 8 publications

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“…Although the gross number of clusters differed between the UniGene sets derived by UIcluster and NCBI, the cluster composition was very similar. Previously reported results demonstrated 2.5-5% difference in cluster composition between the two strategies (26).…”

Section: Gene Discoverymentioning

confidence: 83%

Large-scale gene discovery in human airway epithelia reveals novel transcripts

Scheetz

Zabner²,

Welsh³

et al. 2004

Physiological Genomics

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The airway epithelium represents an important barrier between the host and the environment. It is a first site of contact with pathogens, particulates, and other stimuli, and has evolved the means to dynamically respond to these challenges. In an effort to define the transcript profile of airway epithelia, we created and sequenced cDNA libraries from cystic fibrosis (CF) and non-CF epithelia and from human lung tissue. Sequencing of these libraries produced ∼53,000 3′-expressed sequence tags (3′-ESTs). From these, a nonredundant UniGene set of more than 19,000 sequences was generated. Despite the relatively small contribution of airway epithelia to the total mass of the lung, focused gene discovery in this tissue yielded novel results. The ESTs included several thousand transcripts (6,416) not previously identified from cDNA sequences as expressed in the lung. Among the abundant transcripts were several genes involved in host defense. Most importantly, the set also included 879 3′-ESTs that appear to be novel sequences not previously represented in the National Center for Biotechnology Information UniGene collection. This UniGene set should be useful for studies of pulmonary diseases involving the airway epithelium including cystic fibrosis, respiratory infections and asthma. It also provides a reagent for large-scale expression profiling.

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Section: Gene Discoverymentioning

confidence: 83%

Large-scale gene discovery in human airway epithelia reveals novel transcripts

Scheetz

Zabner²,

Welsh³

et al. 2004

Physiological Genomics

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“…The complexity of the comparison feature in the algorithm is reduced because of the hashing table [21] generated as clusters were formed. In the recent years, the hashing technique is used to speed up the comparison of cDNA sequence because comparing numbers has proved to be much faster than comparing text [22][23].…”

Section: Phase II -Initial Clusteringmentioning

confidence: 99%

“…The clustering algorithm proposed to solve the stated problem in this research is the hashing technique which eliminates the clustering performance issue; meanwhile parallelization approach is used to solve the computational and memory problem. Both techniques were used in clustering of 'Expressed Sequence Tags' (ESTs) from complementary DNA (cDNA) clone libraries [23]. For this research however clusters are grouped together according to scenarios and an individual cluster may be a member to more than one scenario and this computation is done simultaneously.…”

Section: Phase III -Cluster Joiningmentioning

confidence: 99%

An Operational Framework for Alert Correlation using a Novel Clustering Approach

Mohamed¹,

Idris²,

Shanmugum³

2012

IJCA

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Intrusion Detection System (IDS) is a well known security feature and widely implemented among practitioners. However, since the creation of IDS the enormous number of alerts generated by the detection sensors has always been a setback in the implementation environment. Moreover due to this obtrusive predicament, two other problems have emerged which are the difficulty in processing the alerts accurately and also the decrease in performance rate in terms of time and memory capacity while processing these alerts. Thus, based on the specified problems, the purpose of our overall research is to construct a holistic solution that is able to reduce the number of alerts to be processed and at the same time to produce a high quality attack scenarios that are meaningful to the administrators in a timely manner. In this paper we will present our proposed framework together with the result of our novel clustering method, architectured solely with the intention of reducing the amount of alerts generated by IDS. The clustering method was tested against two dataset; a globally used dataset, DARPA and a live dataset from a cyber attack monitoring unit that uses SNORT engine to capture the alerts. The result obtained from the experiment is very promising; the clustering algorithm was able to reduce about 86.9% of the alerts used in the experiment. From the result we are able to highlight the contribution to practitioners in an actual working environment.

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“…The ESTs generated from specific tissues represents the presence of active mRNAs in the selected tissue and sampling conditions. The creation of an EST database has several advantages including a fast and inexpensive way to discover novel genes, rapid identification of active genes, identification of exon–intron structure, generation of information on gene expression, gene regulation and sequence diversity, comparative genomic study, serve as markers or tags for transcripts, development of markers for reference genetic map and recovery of full-length cDNAs and genomic sequences (Ho et al 2007 ; Luro et al 2008 ; Thanh et al 2011 ; Trivedi et al 2003 ; Ye et al 2010 ; Zeng et al 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Expressed sequence tags (ESTs) from young leaves of Metroxylon sagu

Wee

Roslan

2012

3 Biotech

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Sago palm, or Metroxylon sagu, is a hardy and versatile plant that is able to tolerate many stresses, biotic and abiotic, during its growth. It is one of the plants that are able to grow in waterlogged area where others could not. Apart from that sago palm is also a source of starch, contributes economically to the people and an important export for the state of Sarawak. Despite the importance of sago palm especially in the production of starch and its ability to withstand stresses, so far, not many molecular studies have been reported on sago palm. To study the characters in sago palm, transcriptome analysis was conducted where it would give a better understanding of the plant development through gene expression. Here, we report the construction of a cDNA library and preliminary expressed sequence tags analysis from the young leaves of sago palm. A total of 434 clones were sequenced with inserts ranging from 1,000 to 3,000 bps with primary and amplified titers of 8 × 105 and 1.0 × 109 pfu/ml, respectively. Clustering of these sequences resulted in a set of 372 tentative unigenes comprising 340 singletons and 32 contigs. The database was also annotated with BLAST2GO which showed that majority of the transcripts were involved in primary metabolism and stress tolerance.

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Alternative Parallelization Strategies in EST Clustering

Cited by 8 publications

References 8 publications

Large-scale gene discovery in human airway epithelia reveals novel transcripts

Large-scale gene discovery in human airway epithelia reveals novel transcripts

An Operational Framework for Alert Correlation using a Novel Clustering Approach

Expressed sequence tags (ESTs) from young leaves of Metroxylon sagu

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