4 of May 08 for students.ppt

Why we do multiple alignments? Multiple nucleotide or amino sequence alignment techniques are usually performed to fit one of the following scopes : In order to characterize protein families, identify shared regions of homology in a multiple sequence alignment; (this happens generally when a sequence search revealed homologies to several sequences) Determination of the consensus sequence of several aligned sequences. Why we do multiple alignments? Help prediction of the secondary and tertiary structures of new sequences; Preliminary step in molecular evolution analysis using Phylogenetic methods for constructing phylogenetic trees. 与上一章的关系 1、对数据库比较； 2、比较后寻找到一组相似序列； 3、构建进化树 然后进入http://www.ebi.ac.uk/clustalw/ 站点，将需要比较的序列输入工具程序中 ，在图4.1中的“序列输入窗口”输入或粘贴需要比较的序列，也可以在“文件输入窗口”将含有需要比较序列的文件名输入Clustalw运行程序中，进行多序列比较。 F3 PROTEIN DOMAIN FAMILIES Many proteins are built up from domains in a modular architecture模块化结构 . The study of protein families is best pursued as a study of protein domain families. Prodom is a database of protein domain sequences created by automatic means from the protein sequence databases. The resources described in this section can be viewed as protein domain family descriptions. ▲ Domain families These represent complete domain sequences with scores for each amino acid at each position in a multiple alignment, and position specific measures of the likelihood of insertion and deletion. They are used as an alternative to sequence patterns in some PROSITE database entries. ▲ Sequence profiles(序列剖面) Fig. 1. A PROSITE sequence profile (taken with permission from the PROSITE user manual, copyright by Amos Balroch). A multiple alignment segment is shown above the profile. Within the profile, numbers represent scores for each of the amino acids at the corresponding position in the multiple alignment. In the first column, for instance, scores are high for the observed amino acids (F, Y, L), and also for amino acids that substitute well for these (W, V, I, M)