Space and time efficient parallel algorithms and software for EST clustering

Kalyanaraman, Anantharaman; Aluru, Srinivas; Brendel, Volker; Kothari, Suresh

doi:10.1109/tpds.2003.1255634

Cited by 31 publications

(17 citation statements)

References 26 publications

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“…Sequence base calls, vector trimming, and low-quality sequence filtering were performed by the Arizona Genomics Computation Laboratory as described elsewhere (Udall et al, 2006). EST sequences were initially clustered using PaCE (Kalyanaraman et al, 2003) and subsequently assembled using CAP3 (Huang and Madan, 1999). Functional annotations for each EST and contig consensus sequence were generated by BLASTing (Altschul et al, 1990) against the UniProt database with a cutoff of 1 e-10 .…”

Section: Cdna Library Construction For Line MCmentioning

confidence: 99%

Evolution of Cinnamate/p-Coumarate Carboxyl Methyltransferases and Their Role in the Biosynthesis of Methylcinnamate

et al. 2007

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Methylcinnamate, which is widely distributed throughout the plant kingdom, is a significant component of many floral scents and an important signaling molecule between plants and insects. Comparison of an EST database obtained from the glandular trichomes of a basil (Ocimum basilicum) variety that produces high levels of methylcinnamate (line MC) with other varieties producing little or no methylcinnamate identified several very closely related genes belonging to the SABATH family of carboxyl methyltransferases that are highly and almost exclusively expressed in line MC. Biochemical characterization of the corresponding recombinant proteins showed that cinnamate and p-coumarate are their best substrates for methylation, thus designating these enzymes as cinnamate/p-coumarate carboxyl methyltransferases (CCMTs). Gene expression, enzyme activity, protein profiling, and metabolite content analyses demonstrated that CCMTs are responsible for the formation of methylcinnamate in sweet basil. A phylogenetic analysis of the entire SABATH family placed these CCMTs into a clade that includes indole-3-acetic acid carboxyl methyltransferases and a large number of uncharacterized carboxyl methyltransferase-like proteins from monocots and lower plants. Structural modeling and ligand docking suggested active site residues that appear to contribute to the substrate preference of CCMTs relative to other members of the SABATH family. Site-directed mutagenesis of specific residues confirmed these findings.

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Section: Cdna Library Construction For Line MCmentioning

confidence: 99%

Evolution of Cinnamate/p-Coumarate Carboxyl Methyltransferases and Their Role in the Biosynthesis of Methylcinnamate

et al. 2007

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“…This pipeline involves clustering and assembly sequences, which are highly compute intensive. The overlapping sequences among the parts of gene sequences are grouped by software, PaCE [4] that is often run in parallel. The results of this clustering process are then fed to the assembly process to generate contigs, which are the consensus sequences derived from multiple mRNA sequences.…”

Section: Introduction (Heading 1)mentioning

confidence: 99%

SWARM: Scheduling Large-Scale Jobs over the Loosely-Coupled HPC Clusters

Pallickara

Pierce

2008

2008 IEEE Fourth International Conference on eScience

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Abstract-Compute-intensive scientific applications are heavily reliant on the available quantity of computing resources. The Grid paradigm provides a large scale computing environment for scientific users. However, conventional Grid job submission tools do not provide a high-level job scheduling environment for these users across multiple institutions. For extremely large number of jobs, a more scalable job scheduling framework that can leverage highly distributed clusters and supercomputers is required. In this paper, we propose a high-level job scheduling Web service framework, Swarm. Swarm is developed for scientific applications that must submit massive number of high-throughput jobs or workflows to highly distributed computing clusters. The Swarm service itself is designed to be extensible, lightweight, and easily installable on a desktop or small server. As a Web service, derivative services based on Swarm can be straightforwardly integrated with Web portals and science gateways. This paper provides the motivation for this research, the architecture of the Swarm framework, and a performance evaluation of the system prototype.

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“…A parallel clustering method developed at Iowa State University [8], PaCE, uses an implementation of suffix trees for sequence comparison. The method is a strict sequence identity match clustering method and performs an NxN alignment, although in parallel, hence offsetting the high costs associated.…”

Section: Introductionmentioning

confidence: 99%

Alternative Parallelization Strategies in EST Clustering

Trivedi

Pedretti

Braun

et al. 2003

Lecture Notes in Computer Science

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Abstract.One of the fundamental components of large-scale gene discovery projects is that of clustering of Expressed Sequence Tags (ESTs) from complementary DNA (cDNA) clone libraries. Clustering is used to create non-redundant catalogs and indices of these sequences. In particular, clustering of ESTs is frequently used to estimate the number of genes derived from cDNA-based gene discovery efforts. This paper presents a novel parallel extension to an EST clustering program, UIcluster4, that incorporates alternative splicing information and a new parallelization strategy. The results are compared to other parallelized EST clustering systems in terms of overall processing time and in accuracy of the resulting clustering.

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Space and time efficient parallel algorithms and software for EST clustering

Cited by 31 publications

References 26 publications

Evolution of Cinnamate/p-Coumarate Carboxyl Methyltransferases and Their Role in the Biosynthesis of Methylcinnamate

Evolution of Cinnamate/p-Coumarate Carboxyl Methyltransferases and Their Role in the Biosynthesis of Methylcinnamate

SWARM: Scheduling Large-Scale Jobs over the Loosely-Coupled HPC Clusters

Alternative Parallelization Strategies in EST Clustering

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