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140
Integrative genomics viewer
- Nat Biotechnol
, 2011
"... Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole genome sequencing, epigenetic surveys, expression profiling of coding and non-coding RNAs, SNP and copy number profiling, and functional assays. Analys ..."
Abstract
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Cited by 123 (1 self)
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. Analysis of these large, diverse datasets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient
1 Genome Analysis GATB: Genome Assembly & Analysis Tool Box
"... Motivation: Efficient and fast NGS algorithms are essential to ana-lyze the terabytes of data generated by the next generation se-quencing machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and ad-vanced hardware implementation. Results ..."
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. Results: We propose an open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software. The library is based on a recent optimized de-Bruijn graph implementation allowing complex genomes to be processed on desktop computers using fast algorithms
GATB: Genome Assembly & Analysis Tool Box
, 2014
"... Motivation: Efficient and fast next-generation sequencing (NGS) algo-rithms are essential to analyze the terabytes of data generated by the NGS machines. A serious bottleneck can be the design of such algo-rithms, as they require sophisticated data structures and advanced hardware implementation. Re ..."
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. Results: We propose an open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software. The library is based on a recent optimized de-Bruijn graph implementation allowing complex genomes to be processed on desk-top computers using fast algorithms
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
- Bioinformatics
, 2011
"... Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well-documented and efficient, and allows researc ..."
Abstract
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Cited by 9 (1 self)
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Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well-documented and efficient, and allows
Genome analysis Advance Access publication July 1, 2014 GATB: Genome Assembly & Analysis Tool Box
"... Motivation: Efficient and fast next-generation sequencing (NGS) algo-rithms are essential to analyze the terabytes of data generated by the NGS machines. A serious bottleneck can be the design of such algo-rithms, as they require sophisticated data structures and advanced hardware implementation. Re ..."
Abstract
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. Results: We propose an open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software. The library is based on a recent optimized de-Bruijn graph implementation allowing complex genomes to be processed on desk-top computers using fast algorithms
Small Genome Annotation and Data Management at TIGR
"... TIGR has developed, and continues to refine, a comprehensive, efficient system for small genome annotation. The Glimmer gene finding software identifies open reading frames most likely to code for genes. The protein sequences from these genes are searched against a nonredundant protein database, pro ..."
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TIGR has developed, and continues to refine, a comprehensive, efficient system for small genome annotation. The Glimmer gene finding software identifies open reading frames most likely to code for genes. The protein sequences from these genes are searched against a nonredundant protein database
Comprehensively and efficiently protecting the heap
- In Proceedings of the 12th International Conference on Architectural Support for Programming Languages and Operating Systems
, 2006
"... The goal of this paper is to propose a scheme that provides comprehensive security protection for the heap. Heap vulnerabilities are increasingly being exploited for attacks on computer programs. In most implementations, the heap management library keeps the heap meta-data (heap structure informatio ..."
Abstract
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Cited by 18 (0 self)
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The goal of this paper is to propose a scheme that provides comprehensive security protection for the heap. Heap vulnerabilities are increasingly being exploited for attacks on computer programs. In most implementations, the heap management library keeps the heap meta-data (heap structure
SOFTWARE Open Access Software Accessing the SEED Genome Databases via Web Services API: Tools for Programmers
"... Background: The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genome ..."
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Background: The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial
Development Approach and Architecture of GenSAS: the Genome Sequence Annotation Server
"... significantly reduced the costs associated with sequencing an organism’s genome. However, the operating costs of hardware, software, and labor to analyze the sequence data are still too high for most users to process in house. Henceforth, most of the current bioinformatics applications used by bench ..."
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-based genome annotation pipelines, GenSAS is unique in that it offers a one-stop website with a single graphical interface for running multiple structural and functional annotation tools, visualization and manual curation of genome. We present its functionality, the technology used in implementing each
Methods A Complexity Reduction Algorithm for Analysis and Annotation of Large Genomic Sequences
"... DNA is a universal language encrypted with biological instruction for life.In higher organisms, the genetic information is preserved predominantly in an organized exon/intron structure.When a gene is expressed, the exons are spliced together to form the transcript for protein synthesis.We have devel ..."
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showed that CRASA annotation excelled in both the sensitivity and specificity categories.When CRASA was applied to the analysis of human Chromosomes 21 and 22, an additional 83 potential genes were identified.With its large-scale processing capability, CRASA can be used as a robust tool for genome
Results 1 - 10
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140
