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Results 1 - 10
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607
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
- Nucleic Acids Res
, 2003
"... There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic DNA fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally speci®c t ..."
Abstract
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Cited by 133 (5 self)
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with on chip oligonucleotide synthesis, this program makes it feasible to perform expression analysis on a genomic scale for any organism for which the genome sequence is known. This is without relying on cDNA or oligonucleotide libraries. OligoArray 2.0 was used to design 75 764 oligonucleotides representing
PGAP: pan-genomes analysis pipeline
- Bioinformatics
"... Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We ..."
Abstract
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Cited by 18 (2 self)
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Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed
Halvade: scalable sequence analysis with MapReduce”,
, 2015
"... ABSTRACT Motivation: Post-sequencing DNA analysis typically consists of read mapping followed by variant calling. Especially for whole genome sequencing, this computational step is very time-consuming, even when using multithreading on a multi-core machine. Results: We present Halvade, a framework ..."
Abstract
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Cited by 3 (1 self)
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that enables sequencing pipelines to be executed in parallel on a multi-node and/or multicore compute infrastructure in a highly efficient manner. As an example, a DNA sequencing analysis pipeline for variant calling has been implemented according to the GATK Best Practices recommendations, supporting both
Sequence analysis damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets
"... Summary: DamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with nor-malization based on ..."
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Summary: DamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with nor-malization based
SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data
, 2012
"... In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demand ..."
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and pre-processing, (c) sequence alignment to a reference genome, (d) SNP and DIP detection, (e) functional annotation of variants using different approaches, and (f) detailed report generation during various stages of the workflow. The pipeline connects the selected analysis steps, exposes all available
Comprehensive comparative analysis of strand-specific RNA sequencing methods
- Nat. Methods
, 2010
"... Strand-specific, massively-parallel cDNA sequencing (RNA-Seq) is a powerful tool for novel transcript discovery, genome annotation, and expression profiling. Despite multiple published methods for strand-specific RNA-Seq, no consensus exists as to how to choose between them. Here, we developed a com ..."
Abstract
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Cited by 40 (4 self)
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Strand-specific, massively-parallel cDNA sequencing (RNA-Seq) is a powerful tool for novel transcript discovery, genome annotation, and expression profiling. Despite multiple published methods for strand-specific RNA-Seq, no consensus exists as to how to choose between them. Here, we developed a
DDBJ Read Annotation Pipeline: ACloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data
, 2013
"... High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecu-lar biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japa ..."
Abstract
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High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecu-lar biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank
• ReCPU: a Parallel and Pipelined Architecture for Regular Expression Matching [2]
"... Text pattern matching is one of the main and most computation intensive parts of systems such as Network Intrusion Detection Systems and DNA Sequencing Matching. Soft- ware solutions to this are available but often they do not satisfy the requirements in terms of performance. This pa- per presents a ..."
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Text pattern matching is one of the main and most computation intensive parts of systems such as Network Intrusion Detection Systems and DNA Sequencing Matching. Soft- ware solutions to this are available but often they do not satisfy the requirements in terms of performance. This pa- per presents
E-Gene - A modular and configurable pipeline system for automated DNA sequence analysis
"... DNA reads generated by large-scale sequencing projects have to be processed before further analyses in order to perform vector/primer masking, low-quality trimming and contaminant removal. This sequential processing involves several steps and the use of different computer programs, each one followin ..."
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before they can be properly configured. Some others are more specialized to perform determined functions [1,2], not allowing the incorporation of new modules in an integrated way. This paper reports the development of E-Gene, an integrated system that makes pipeline construction a modular job. We have
Cloudenabling Sequence Alignment with Hadoop MapReduce: A Performance Analysis. IPCBEE
, 2012
"... Abstract. The Bio Sequence alignment involves arranging DNA, RNA or protein sequences in order to find similarity between the aligned sequences, which helps us to find the structural, functional and evolutionary relationships among organisms. Next generation sequencing has led to the generation of b ..."
Abstract
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Cited by 1 (0 self)
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of billions of sequence data, making it increasingly infeasible for sequence alignment to be performed on standalone machines. Hence algorithms capable of running in multi-node clusters and deployable on cloud have been investigated. The performance improvement offered by these algorithms is not usually
Results 1 - 10
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607
