检索结果-内蒙古大学图书馆

ContextMap 2: fast and accurate context-based RNA-seq mapping

BMC BIOINFORMATICS 2015年第1期16卷 1-15页

作者： Bonfert, Thomas Kirner, Evelyn Csaba, Gergely Zimmer, Ralf Friedel, Caroline C. Univ Munich Inst Informat D-80333 Munich Germany

Background: Mapping of short sequencing reads is a crucial step in the analysis of RNA sequencing (RNA-seq) data. ContextMap is an RNA-seq mapping algorithm that uses a context-based approach to identify the best alignment for each read and allows parallel mapping against several reference genomes. Results: In this article, we present ContextMap 2, a new and improved version of ContextMap. Its key novel features are: (i) a plug-in structure that allows easily integrating novel short read alignment programs with improved accuracy and runtime;(ii) context-based identification of insertions and deletions (indels);(iii) mapping of reads spanning an arbitrary number of exons and indels. ContextMap 2 using Bowtie, Bowtie 2 or BWA was evaluated on both simulated and real-life data from the recently published RGASP study. Conclusions: We show that ContextMap 2 generally combines similar or higher recall compared to other state-of-the-art approaches with significantly higher precision in read placement and junction and indel prediction. Furthermore, runtime was significantly lower than for the best competing approaches. ContextMap 2 is freely available at http://***/ContextMap.

关键词： Splice Site Splice Junction alignment program Seed Length Read alignment

来源：评论

学校读者我要写书评

暂无评论

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C_α only models, Alternative alignments, and Non-sequential alignments

引用

BMC BIOINFORMATICS 2013年第1期14卷 1-22页

作者： Minami, Shintaro Sawada, Kengo Chikenji, George Nagoya Univ Dept Computat Sci & Engn Nagoya Aichi 4648603 Japan Nagoya Univ Dept Appl Phys Nagoya Aichi 4648603 Japan

Background: Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Further investigation of such protein relationships would give us a hint as to how proteins can change their fold in the course of evolution, as well as a insight into physico-chemical properties of secondary structure packing. For this purpose, highly accurate sequence order independent structure comparison methods are needed. Results: We have developed a novel protein structure alignment algorithm, MICAN (a structure alignment algorithm that can handle Multiple-chain complexes, Inverse direction of secondary structures, C-alpha only models, Alternative alignments, and Non-sequential alignments). The algorithm was designed so as to identify the best structural alignment between protein pairs by disregarding the connectivity between secondary structure elements (SSE). One of the key feature of the algorithm is utilizing the multiple vector representation for each SSE, which enables us to correctly treat bent or twisted nature of long SSE. We compared MICAN with other 9 publicly available structure alignment programs, using both reference-dependent and reference-independent evaluation methods on a variety of benchmark test sets which include both sequential and non-sequential alignments. We show that MICAN outperforms the other existing methods for reproducing reference alignments of non-sequential test sets. Further, although MICAN does not specialize in sequential structure alignment, it showed the top level performance on the sequential test sets. We also show that MICAN program is the fastest non-sequential structure alignment program among all the programs we examined here. Conclusions: MICAN is the fastest and the most accurate program among non-sequential alignment programs we examined here. These results suggest that MICAN is a highly effective

关键词： Root Mean Square Deviation Secondary Structure Element Protein Pair alignment program Reference alignment

来源：评论

学校读者我要写书评

暂无评论

Efficient digest of high-throughput sequencing data in a reproducible report

引用

BMC BIOINFORMATICS 2013年第Sup11期14卷 S3-S3页

作者： Zhang, Zhe Leipzig, Jeremy Sasson, Ariella Yu, Angela M. Perin, Juan C. Xie, Hongbo M. Sarmady, Mahdi Warren, Patrick V. White, Peter S. Childrens Hosp Philadelphia Ctr Biomed Informat Philadelphia PA 19104 USA Childrens Hosp Philadelphia Div Oncol Philadelphia PA USA Univ Penn Dept Pediat Perelman Sch Med Philadelphia PA 19104 USA

Background: High-throughput sequencing (HTS) technologies are spearheading the accelerated development of biomedical research. Processing and summarizing the large amount of data generated by HTS presents a nontrivial challenge to bioinformatics. A commonly adopted standard is to store sequencing reads aligned to a reference genome in SAM (Sequence alignment/Map) or BAM (Binary alignment/Map) files. Quality control of SAM/BAM files is a critical checkpoint before downstream analysis. The goal of the current project is to facilitate and standardize this process. Results: We developed bamchop, a robust program to efficiently summarize key statistical metrics of HTS data stored in BAM files, and to visually present the results in a formatted report. The report documents information about various aspects of HTS data, such as sequencing quality, mapping to a reference genome, sequencing coverage, and base frequency. Bamchop uses the R language and Bioconductor packages to calculate statistical matrices and the Sweave utility and associated LaTeX markup for documentation. Bamchop's efficiency and robustness were tested on BAM files generated by local sequencing facilities and the 1000 Genomes Project. Source code, instruction and example reports of bamchop are freely available from https://***/CBMi-BiG/bamchop. Conclusions: Bamchop enables biomedical researchers to quickly and rigorously evaluate HTS data by providing a convenient synopsis and user-friendly reports.

关键词： Read Count Sequencing Depth Sequencing Quality alignment program Bioconductor Project

来源：评论

学校读者我要写书评

暂无评论

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

引用

BMC BIOINFORMATICS 2012年第1期13卷 1-8页

作者： Daniels, Noah M. Nadimpalli, Shilpa Cowen, Lenore J. Tufts Univ Dept Comp Sci Medford MA 02155 USA Princeton Univ Dept Comp Sci Princeton NJ 08540 USA

Background: The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results: We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs;depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions: Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

关键词： Structural alignment alignment program Conservation Score Core Length alignment Quality

来源：评论

学校读者我要写书评

暂无评论

Cgaln: fast and space-efficient whole-genome alignment

引用

BMC BIOINFORMATICS 2010年第1期11卷 1-14页

作者： Nakato, Ryuichiro Gotoh, Osamu Kyoto Univ Grad Sch Informat Dept Intelligence Sci & Technol Sakyo Ku Kyoto 6068501 Japan Univ Tokyo Inst Mol & Cellular Biosci Bunkyo Ku Tokyo 1130032 Japan Natl Inst Adv Ind Sci & Technol Computat Biol Res Ctr Koto Ku Tokyo 1350064 Japan

Background: Whole-genome sequence alignment is an essential process for extracting valuable information about the functions, evolution, and peculiarities of genomes under investigation. As available genomic sequence data accumulate rapidly, there is great demand for tools that can compare whole-genome sequences within practical amounts of time and space. However, most existing genomic alignment tools can treat sequences that are only a few Mb long at once, and no state-of-the-art alignment program can align large sequences such as mammalian genomes directly on a conventional standalone computer. Results: We previously proposed the CGAT (Coarse-Grained alignment) algorithm, which performs an alignment job in two steps: first at the block level and then at the nucleotide level. The former is "coarse-grained" alignment that can explore genomic rearrangements and reduce the sizes of the regions to be analyzed in the next step. The latter is detailed alignment within limited regions. In this paper, we present an update of the algorithm and the open-source program, Cgaln, that implements the algorithm. We compared the performance of Cgaln with those of other programs on whole genomic sequences of several bacteria and of some mammalian chromosome pairs. The results showed that Cgaln is several times faster and more memory-efficient than the best existing programs, while its sensitivity and accuracy are comparable to those of the best programs. Cgaln takes less than 13 hours to finish an alignment between the whole genomes of human and mouse in a single run on a conventional desktop computer with a single CPU and 2 GB memory. Conclusions: Cgaln is not only fast and memory efficient but also effective in coping with genomic rearrangements. Our results show that Cgaln is very effective for comparison of large genomes, especially of intact chromosomal sequences. We believe that Cgaln provides novel viewpoint for reducing computational complexity and will contribute to various

关键词： Dynamic programming Block Size Input Sequence alignment program Global alignment

来源：评论

学校读者我要写书评

暂无评论

Towards realistic benchmarks for multiple alignments of non-coding sequences

引用

BMC BIOINFORMATICS 2010年第1期11卷 54-54页

作者： Kim, Jaebum Sinha, Saurabh Univ Illinois Dept Comp Sci Urbana IL 61801 USA Univ Illinois Inst Genom Biol Urbana IL 61801 USA

Background: With the continued development of new computational tools for multiple sequence alignment, it is necessary today to develop benchmarks that aid the selection of the most effective tools. Simulation-based benchmarks have been proposed to meet this necessity, especially for non-coding sequences. However, it is not clear if such benchmarks truly represent real sequence data from any given group of species, in terms of the difficulty of alignment tasks. Results: We find that the conventional simulation approach, which relies on empirically estimated values for various parameters such as substitution rate or insertion/deletion rates, is unable to generate synthetic sequences reflecting the broad genomic variation in conservation levels. We tackle this problem with a new method for simulating non-coding sequence evolution, by relying on genome-wide distributions of evolutionary parameters rather than their averages. We then generate synthetic data sets to mimic orthologous sequences from the Drosophila group of species, and show that these data sets truly represent the variability observed in genomic data in terms of the difficulty of the alignment task. This allows us to make significant progress towards estimating the alignment accuracy of current tools in an absolute sense, going beyond only a relative assessment of different tools. We evaluate six widely used multiple alignment tools in the context of Drosophila non-coding sequences, and find the accuracy to be significantly different from previously reported values. Interestingly, the performance of most tools degrades more rapidly when there are more insertions than deletions in the data set, suggesting an asymmetric handling of insertions and deletions, even though none of the evaluated tools explicitly distinguishes these two types of events. We also examine the accuracy of two existing tools for annotating insertions versus deletions, and find their performance to be close to optimal in Drosophila non

关键词： Drosophila Species alignment program True alignment Root Sequence alignment Task

来源：评论

学校读者我要写书评

暂无评论

Application of 'next-generation' sequencing technologies to microbial genetics

引用

NATURE REVIEWS MICROBIOLOGY 2009年第4期7卷 287-296页

作者： MacLean, Daniel Jones, Jonathan D. G. Studholme, David J. Sainsbury Lab Norwich NR4 7UH Norfolk England

New sequencing methods generate data that can allow the assembly of microbial genome sequences in days. With such revolutionary advances in technology come new challenges in methodologies and informatics. In this article, we review the capabilities of high-throughput sequencing technologies and discuss the many options for getting useful information from the data.

关键词： SHORT DNA-SEQUENCES alignment program MESSENGER-RNA SHORT READS GENOME EXPRESSION ARABIDOPSIS TOOL SEQ INFORMATION

来源：评论

学校读者我要写书评

暂无评论

Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty

引用

BMC BIOINFORMATICS 2009年第s3期10卷 S1-S1页

作者： Agrawal, Ankit Huang, Xiaoqiu Iowa State Univ Dept Comp Sci Ames IA 50011 USA

Background: Accurate estimation of statistical significance of a pairwise alignment is an important problem in sequence comparison. Recently, a comparative study of pairwise statistical significance with database statistical significance was conducted. In this paper, we extend the earlier work on pairwise statistical significance by incorporating with it the use of multiple parameter sets. Results: Results for a knowledge discovery application of homology detection reveal that using multiple parameter sets for pairwise statistical significance estimates gives better coverage than using a single parameter set, at least at some error levels. Further, the results of pairwise statistical significance using multiple parameter sets are shown to be significantly better than database statistical significance estimates reported by BLAST and PSI-BLAST, and comparable and at times significantly better than SSEARCH. Using non-zero parameter set change penalty values give better performance than zero penalty. Conclusion: The fact that the homology detection performance does not degrade when using multiple parameter sets is a strong evidence for the validity of the assumption that the alignment score distribution follows an extreme value distribution even when using multiple parameter sets. Parameter set change penalty is a useful parameter for alignment using multiple parameter sets. Pairwise statistical significance using multiple parameter sets can be effectively used to determine the relatedness of a (or a few) pair(s) of sequences without performing a time-consuming database search.

关键词： alignment program alignment Score Substitution Matrice Progressive Multiple Sequence alignment Pairwise Sequence alignment

来源：评论

学校读者我要写书评

暂无评论

Automatic extraction of reliable regions from multiple sequence alignments

引用

BMC BIOINFORMATICS 2007年第s5期8卷 1-7页

作者： Lassmann, Timo Sonnhammer, Erik L. L. Karolinska Inst Dept Cell & Mol Biol SE-17177 Stockholm Sweden Univ Stockholm Bioinformat Ctr S-10691 Stockholm Sweden

Background: High quality multiple alignments are crucial in the transfer of annotation from one genome to another. Multiple alignment methods strive to achieve ever increasing levels of average accuracy on benchmark sets while the accuracy of individual alignments is often overlooked. Results: We have previously developed a method to automatically assess the accuracy and overall difficulty of multiple alignments. This was achieved by a per-residue comparison between alternate alignments of the same sequences. Here we present a key extension to this method, an algorithm to extract similarly aligned regions from several alignments and merge them into a new consensus alignment. Conclusion: We demonstrate that the fraction of correctly aligned residues within the resulting alignments is increased by 25-100 percent compared to the original input alignments, as only the most reliably aligned parts are considered.

关键词： Multiple alignment alignment Method alignment program Reliability Score alignment Accuracy

来源：评论

学校读者我要写书评

暂无评论

An enhanced RNA alignment benchmark for sequence alignment programs

引用

ALGORITHMS FOR MOLECULAR BIOLOGY 2006年第0期1卷 19-19页

作者： Wilm, Andreas Mainz, Indra Steger, Gerhard Univ Dusseldorf Inst Phys Biol D-40225 Dusseldorf Germany

Background: The performance of alignment programs is traditionally tested on sets of protein sequences, of which a reference alignment is known. Conclusions drawn from such protein benchmarks do not necessarily hold for the RNA alignment problem, as was demonstrated in the first RNA alignment benchmark published so far. For example, the twilight zone - the similarity range where alignment quality drops drastically - starts at 60 % for RNAs in comparison to 20 % for proteins. In this study we enhance the previous benchmark. Results: The RNA sequence sets in the benchmark database are taken from an increased number of RNA families to avoid unintended impact by using only a few families. The size of sets varies from 2 to 15 sequences to assess the influence of the number of sequences on program performance. alignment quality is scored by two measures: one takes into account only nucleotide matches, the other measures structural conservation. The performance order of parameters - like nucleotide substitution matrices and gap-costs - as well as of programs is rated by rank tests. Conclusion: Most sequence alignment programs perform equally well on RNA sequence sets with high sequence identity, that is with an average pairwise sequence identity (APSI) above 75 %. Parameters for gap-open and gap-extension have a large influence on alignment quality lower than APSI <= 75 %;optimal parameter combinations are shown for several programs. The use of different 4 x 4 substitution matrices improved program performance only in some cases. The performance of iterative programs drastically increases with increasing sequence numbers and/or decreasing sequence identity, which makes them clearly superior to programs using a purely non-iterative, progressive approach. The best sequence alignment programs produce alignments of high quality down to APSI > 55 %;at lower APSI the use of sequence+structure alignment programs is recommended.

关键词： alignment program Substitution Matrix alignment Quality Reference alignment Substitution Matrice

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：