suc生物信息软件综合实践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 * /pmc/articles/PMC540061/ A hypothetical gene tree and the resulting Inparanoid clusters are shown to illustrate inparalog (and thus co-ortholog) and outparalog assignments. (a) Protein A in an ancestral species ‘A’ undergoes a gene duplication. A speciation event occurs which gives rise to the two lineages leading to species ‘B’ and ‘C’. In the C genome the genes?C2?and?C3?are inparalogs since their gene duplication occurred after speciation; they are co-orthologous to the?B2?gene (one common ancestral protein upon speciation).?B1?is an outparalog of the?C2?and?C3?genes, as are?B1?of?B2?(duplication and divergence prior to speciation). (b)?B2?and?C2?are the original seed-ortholog pair (all inparalogs are clustered around this pair), thus both receiving an inparalog score of 1.0. Other inparalo