华中农业大学生物信息学课件Bioinf05.pptVIP

* * * * * * The input for ClustalW is limited to a maximum of 500 sequences or to a 1MB file (whichever is smaller).? ClustalW needs unique sequence identifiers, which it defines as the first word on the sequence identifier line.? The Scores Table shows the pairwise scores calculated for every pair of sequences that is to be aligned. Pairwise scores are simply the number of identities between the two sequences, divided by the length of the alignment, and represented as a percentage.? The program accepts nucleic acid or protein sequences, in the following multiple sequence formats: NBRF/PIR EMBL/UniProt Pearson (FASTA) GDE ALN/ClustalW GCG/MSF RSF (see the Clustal help pages for details about formats) * * * * * * * * * * * * * * * 由于同一位点多重替代（multiple substitution）的发生，观测到的差异比实际替代数要小 原始序列 后代序列 13 mutations = 3 differences Degree of divergence Total number of substitutions 为了估算出正确的分歧时间（期望替代数），必须对观测到的替代数进行校正 在进化的任意时间点，任意位点的核苷酸都可能发生回复和平行突变。 核苷酸替代模型 Substitution model 观察到的A-T，随着时间增加， A-N-T的可能性增大 * * 主要应用于分析基因或蛋白质的进化 通过分析多个基因或蛋白质序列之间的同源性确定它们在进化上的关系 分析基因家族中新成员的翻译起始位点和内含子（预测的氨基酸序列的对位排列分析） 分析基因或蛋白质的功能 * * * /books/NBK62051/def-item/blast_glossary.orthologs/?report=objectonly * * * ClustalW为命令行版本，ClustalX为图形界面版，两者内核相同 Clustal Omega目前仅有命令行版本 * * BLOSUM (Henikoff). These matrices appear to be the best available for carrying out data base similarity (homology searches). The matrices currently used are: Blosum 80, 62, 45 and 30. BLOSUM was the default in earlier Clustal X versions. PAM (Dayhoff). These have been extremely widely used since the late 70s. We currently use the PAM 20, 60, 120, 350 matrices. GONNET. These matrices were derived using almost the same procedure as the Dayhoff one (above) but are much more up to date and are based on a far larger data set. They appear to be more sensitive than the Dayhoff series. We currently use the GONNET 80, 120, 160, 250 and 350 matrices. This series is the default for Clustal X version 1.8. ClustalX根据序列间的平均一致性根据文件CLUSTAL_SER