PAIRWISE AND SEARCHWISE - FINDING THE OPTIMAL ALIGNMENT IN A SIMULTANEOUS COMPARISON OF A PROTEIN PROFILE AGAINST ALL DNA TRANSLATION FRAMES

Birney E; Thompson JD; Gibson TJ

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PAIRWISE AND SEARCHWISE - FINDING THE OPTIMAL ALIGNMENT IN A SIMULTANEOUS COMPARISON OF A PROTEIN PROFILE AGAINST ALL DNA TRANSLATION FRAMES

机译：对和搜索-在同时针对所有DNA转录框架的蛋白质谱中寻找最佳同源性

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DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide RNA editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal frameshifting during translation. Frameshifts frequently confound computational activities involving homologous sequences, such as database searches and inferences on structure, function or phylogeny made from multiple alignments, A dynamic alignment algorithm is reported here which compares a protein profile (a residue scoring matrix for one or more aligned sequences) against the three translation frames of a DNA strand, allowing frameshifting. The algorithm has been incorporated into a new package, WiseTools, for comparison of biological sequences. A protein profile can be compared against either a DNA sequence or a protein sequence, The program PairWise may be used interactively for alignment of any two sequence inputs, SearchWise can perform combinations of searches through DNA or protein databases by a protein profile or DNA sequence, Routine application of the programs has revealed a set of database entries with frameshifts caused by errors in sequence determination.

机译：DNA翻译框架可能由于多种原因而被破坏，包括：（i）序列确定错误; （ii）RNA加工，例如内含子的去除和指导RNA的编辑; （iii）较不常见的是转录过程中聚合酶移码或翻译过程中核糖体移码。移码经常混淆涉及同源序列的计算活动，例如数据库搜索和对来自多个比对的结构，功能或系统发育的推断。此处报道了一种动态比对算法，该算法比较了蛋白质谱（一个或多个比对序列的残基评分矩阵）与DNA链的三个翻译框架相对应，从而允许移码。该算法已合并到新的软件包WiseTools中，用于比较生物学序列。可以将蛋白质图谱与DNA序列或蛋白质序列进行比较。程序PairWise可以交互地用于任何两个序列输入的比对，SearchWise可以通过蛋白质图谱或DNA序列通过DNA或蛋白质数据库执行搜索组合，程序的常规应用揭示了一组数据库条目，这些条目由于序列确定中的错误而导致了移码。

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《Nucleic Acids Research》 |1996年第14期|共10页
作者
Birney E; Thompson JD; Gibson TJ;
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正文语种 eng
中图分类细胞形态学;生物化学;
关键词
Molecular sequence accuracy; Amino acid substitution; Coding regions; Escherichia coli; Domain; Vav; Identification; Algorithm; Errors; Gene;

机译：分子序列准确性;氨基酸取代;编码区;大肠杆菌;域;Vav;鉴定;算法;错误;基因;

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1. PAIRWISE AND SEARCHWISE - FINDING THE OPTIMAL ALIGNMENT IN A SIMULTANEOUS COMPARISON OF A PROTEIN PROFILE AGAINST ALL DNA TRANSLATION FRAMES [J] . Birney E, Thompson JD, Gibson TJ Nucleic Acids Research . 1996,第14期

机译：对和搜索-在同时针对所有DNA转录框架的蛋白质谱中寻找最佳同源性
2. Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments [J] . Michael L Sierk, Michael E Smoot, Ellen J Bass, BMC Bioinformatics . 2010,第1期

机译：使用接近最佳的蛋白质序列比对提高成对的序列比对准确性
3. Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons [J] . Yonatan Bilu, Pankaj K. Agarwal, Rachel Kolodny IEEE/ACM transactions on computational biology and bioinformatics . 2006,第期

机译：基于成对比较的最优多序列比对的更快算法
4. EUKARYOTIC PROTEIN SUBCELLULAR LOCALIZATION BASED ON LOCAL PAIRWISE PROFILE ALIGNMENT SVM [C] . Jian Guo, Man-Wai Mak, Sun-Yuan Kung IEEE Workshop on Machine Learning for Signal Processing . 2006

机译：基于局部成对轮廓对准SVM的真核蛋白亚细胞定位
5. Enhancing and Evaluating Global Pairwise Alignment of Protein-Protein Interaction Networks. [D] . Elmsallati, Ahed Ashur. 2017

机译：增强和评估蛋白质-蛋白质相互作用网络的全局成对比对。
6. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. [O] . E Birney, J D Thompson, T J Gibson 1996

机译：PairWise和SearchWise：在同时比较蛋白质谱和所有DNA翻译框架时找到最佳比对。
7. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. [O] . Birney, E, Thompson, J D, Gibson, T J 1996

机译：PairWise和SearchWise：在同时比较蛋白质谱和所有DNA翻译框架时找到最佳比对。
8. Exact Simultaneous Confidence Intervals for Pairwise Comparisons of Three Normal Means [R] . Spurrier, J. D., Isham, S. P. 1984

机译：三种正规方法成对比较的精确同时置信区间

PAIRWISE AND SEARCHWISE - FINDING THE OPTIMAL ALIGNMENT IN A SIMULTANEOUS COMPARISON OF A PROTEIN PROFILE AGAINST ALL DNA TRANSLATION FRAMES

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