alignment

专利名称：ALIGNMENT发明人：HAMAZAKI FUMYOSHI,IGARASHI HAJIME,NAKAI AKYA,AYADA NAOKI 申请号：JP6433287申请日：19870320公开号：JPH0468767B2公开日：19921104专利内容由知识产权出版社提供摘要：PURPOSE:To improve accuracy of alignment, by performing measurement in a substituted region when abnormal values are detected in the amount of shift of an original plate to a substrate in prescribed regions on the substrate and performing theta directional alignment of the substrate on the basis of the results of measurement and next performing alignment of the original plate to the substrate in the respective regions. CONSTITUTION:The amount of position shift of an original plate RT to a substrate WF in prescribed regions on the substrate WF is measured by observing light which transmits a projection optical system LN and is reflected on or diffracted from marks on the substrate WF. When abnormal values are detected from the measurement, a substituted region is automatically selected and the measurement is performed in the substituted region. theta directional alignment of the substrate WF is performed on the basis of the results of measurement, and next alignment of the original plate RT to the substrate WF is performed in their respective regions. Hence, following alignment is performed on the basis of the measured values which are high in reliability in the substituted region, and so the alignment of the original plate to the substrate can be performed with good accuracy.申请人：CANON KK更多信息请下载全文后查看。

BAliBASE: A benchmark alignment database for the evaluation of multiplealignment programsJulie D. Thompson, Fridiric Plewniak and Olivier Poch.Institut de Ginitique et de Biologie Moliculaire et Cellulaire,(CNRS/INSERM/ULP), B.P. 163, 67404 Illkirch Cedex, France.E-mail : julie@igbmc.u-strasbg.frIn recent years improvements to existing alignment programs and the introduction of new iterative algorithms have changed the state-of-the-art in multiple sequence alignment. In spite of the wide variety of alignment programs now available, there have been few comparisons of the relative performance and reliability.BAliBASE (1) is a database of manually-refined multiple sequence aligment specifically designed for the evaluation and comparison of multiple alignment programs. The reference alignments are categorised by core blocks of conservation, sequence length, similarity, and presence of insertions and N/C-terminal extensions. The sequences included in the database are selected from structural databases or from manually constructed alignments in the literature. The alignments are manually verified and adjusted, to ensure that conserved residues are aligned as well as the secondary structure elements.BAliBASE (version 1.0) consists of 142 reference alignments, containing over 1000 sequences. The alignments are divided into 4 hierarchical reference sets, reference 1 providing the basis for construction of the following sets. Each of the main sets may be further sub-divided into smaller groups, according to sequence length and percent similarity. Reference 1 contains alignments of (less than 6) equi-distant, similar length sequences. Reference 2 aligns up to three "orphan" sequences (<25% identical) with at least 15 closely related sequences. Reference 3 consists of up to 4 sub-groups, with less than 25% residue identity between sub-groups. Reference 4 contains alignments including N/C-terminal extensions (up to 400 residues), or internal insertions (up to 100 residues).A comparison of alignment programs (2) using the BAliBASE alignments has shown that the choice of an alignment program depends on the sequence set to be aligned, and no single *best9 program exists. It was demonstrated that the twilight zone still exists as a real barrier for all of the programs in the study, but that the best programs were still capable of aligning on average 47% of the residues below the twilight zone at 10-20% residue identity. The recently developed iterative programs often offered improved alignment accuracy although a heavy time penalty was incurred.A notable exception was the effect of introducing a single divergent sequence into a set of closely related sequences, causing the iteration to diverge away from the best alignment. Global alignment algorithms generally performed better than local methods except in the presence of large terminal extensions and internal insertions. In these cases, a local algorithm was more successful in identifying the most conserved motifs. Global programs which tend to favour a collinear alignment of the entire lengths of the sequences were less successful, often producing a total misalignment. None of the alignment programs in the study were capable of producing good, reliable alignments in all of the BAliBASE reference tests.The results of the study should allow users to select the most suitable program depending on the set of sequences to be aligned, thus improving the accuracy of the automatic alignment and reducing the manual refinement required to obtain the final, optimal alignment. The results also indicate guidelines for the future development of multiple alignment programs.References1.Thompson, J.D., Plewniak, F. and Poch,O. (1999) Bioinformatics 1, 87-88.2.Thompson, J.D., Plewniak, F. and Poch,O. (1999) Nucl. Acids Res., (in press)。

alignment with用法alignment with用法Alignment with是一种表达方式，用来描述一个事物与另一个事物之间的对齐或一致性关系。

在创作中，我们可以使用alignmentwith来表达各种不同的概念和含义。

下面是alignment with的几种常见用法及其详细讲解：1. Alignment with目标在这种用法中，alignment with表示某个事物与目标之间的一致性。

例如：•The company’s strategy is in alignment with its long-term goals.•Our actions should be in alignment with our values.在这些例子中，alignment with表示行动或策略与目标保持一致，即保持内外部的协调和一致性。

2. Alignment with利益在这种用法中，alignment with表示某个事物与利益之间的对齐。

例如：•The new policy is in alignment with the interests of both employees and stakeholders.•The government’s decision is not in alignment with the interests of small businesses.这种用法下的alignment with表示某个决策、政策或行为是否符合各方的利益，是否对各方都有好处。

3. Alignment with价值观在这种用法中，alignment with表示某个事物与价值观之间的一致性。

例如：•The candidate’s stance on environmental issues is in alignment with the party’s values.•The company’s commitment to diversity is in alignment with its core values.此用法下的alignment with表示某个行动、决策或行为是否符合某个组织或个人的价值观。

对对齐(alignment)的一些认识关于内存地址对齐，尤其是struct中成员的对齐导致的struct的size问题很多人(包括我:()似乎都没有一个比较清晰的认识，所以产生了整理这方面思路和帖子的想法，下面的文字是资料、文档、实验和推测的混合体，有错误是肯定的:)。

能给您提供一点帮助，是我最大的愿望。

(有点麻了)引：struct s {char c;int i;}; 在sizeof(char)=1 sizeof(int)=4的情况下sizeof(struct s)为什么经常是8不是5？这个就是对齐(alignment)的缘故。

那么什么是对齐？现代计算机中内存空间都是按照byte划分的，从理论上讲似乎对任何类型的变量的访问可以从任何地址开始，但实际情况是在访问特定变量的时候经常在特定的内存地址访问，这就是对齐。

为什么呢？msdn for vc6中有这么一段：This principle is especially important when you write code for porting to multiple processors. A misaligned 4-byte data member, which is on an address that is not a multiple of four, causes a performance penalty with an 80386 processor and a hardware exception with a MIPS&#174; RISC processor. In the latter case, although the system handles the exception, the performance penalty is significantly greater.大意是：1.某些硬件平台只能在某些地址处取某些特定类型的数据，否则抛出硬件异常。