研究プロジェクトの関連で、ちょっと横道に逸れます。MLSTとeBURST Studyについて、復習を進めます。
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eBURST3のサイトhttp://eburst.mlst.netからeBURST3について、細かいところも含めて把握しておこう。2. Defining groupsを抄読する。
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The definition of the group can be changed, but the default eBURST setting is to identify groups of related STs using the most stringent (conservative) definition, where all members assigned to the same group share identical alleles at ? 6 of the 7 loci with at least one other member of the group. |
7つの遺伝子座のうち、6つのアレルが同一であった場合は、同じグループとするというのが厳格なデフォルト設定。一方、ゆるい基準では、7つの遺伝子座のうち、5つのアレルが同一であった場合に同一グループと判定する。
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A less stringent approach is to define the groups by the sharing of alleles at ? 5 of the 7 loci. Whatever group definition is used, this approach results in non- overlapping groups; no ST can be assigned to more than one group. |
いずれにせよ、上記方法では、分類しきれないno STが一つ以上のグループとして存在し得る。
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A ’group’ is used here as a neutral term for the collection of STs that are placed together by eBURST, according to the selected group definition, whereas a clonal complex is a set of STs that are all believed to be descended from the same founding genotype. |
グループとは、eBURSTで一緒になった複数のST集合を指す”自然な”用語として用いられ、一方、Clonal Complexは、同じの遺伝子型が由来と考えられるSTのセット集合を指す。
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Using the stringent group definition (6/7 shared alleles), isolates in the group defined by eBURST will be considered to belong to a single clonal complex. With a less stringent group definition (e.g. 5/7 shared alleles) all of the STs in an eBURST group cannot be assumed to belong to a single clonal complex. |
6/7法では、同一グループに分類された分離株は、一つのClonal Complexに属すると考えられるが、5/7法では、eBURSTのグループが、同一のClonal Complexかどうかは、必ずしもそうならない。
3. Identifying the founder of a group and the patterns of evolutionary descent
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The following description of eBURST focuses on groups identified using the stringent default setting, where all STs must be a single locus variant (SLV) of at least one other ST in the group, and eBURST produce a diagram where all STs in the group are linked (a clonal complex). The use of eBURST with the more relaxed group definition of 5/7 shared alleles is discussed later. |
6/7法では、すべてのSTは、グループ内の他の一つのSTのa single locus variant (SLV) であり、eBURSTは、すべてのSTをclonal clomplexとしてリンクする。
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The primary founder of a group is defined as the ST that differs from the largest number of other STs at only a single locus (i.e. the ST that has the greatest number of single-locus variants; SLVs). This method of assigning the primary founder takes account of the way in which clones emerge and diversify (Figure 1A); |
プライマリーfounder(起源となる株）は、単一の遺伝子座において、もっともたくさんの他のSTグループがあるものと定義される。
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the initial diversification of the founding genotype of a clonal complex will result in variants of the founder that differ at only one of the seven loci (i.e., SLVs of the founder). If two STs have the same number of associated SLVs, the one with the greatest number of double-locus variants (DLVs) is selected as the founding ST. In such cases the confidence in the assignment of the primary founder will be low, as reflected in the bootstrap values (see section 5). |
もし、２つのSTが同じ数のSLVであれば、Double locus variantsの数が大きい方がプライマリーfounderとして選択される。
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The eBURST diagrams display the patterns of descent within each group from the predicted founding ST (Figure 1B). eBURST uses lines to show the radial links from the founder to each of its SLVs. Only SLV links are shown in eBURST, and DLVs of the founder will therefore only be linked if the intermediate SLV on the path from the founder to the DLV is present in the input data. All isolates that are directly linked on a eBURST diagram will therefore differ at only a single locus and the cluster of linked STs should represent a clonal complex. A DLV of the predicted primary founder of a group will not be included if the linking SLV has not been sampled and using the stringent (conservative) default group definition some STs that might be part of the clonal complex will therefore not be shown. In the eBURST diagram, the circle representing the predicted primary founder is coloured blue and the areas of each of the circles indicate the prevalence of the ST in the input data (Figure 1B). |
4. Subgroups and subgroup founders
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In larger eBURST groups there may be several STs besides the predicted primary founder that have a number of SLVs of their own. For example, a SLV of the primary founder may have become successful and diversified to produce its own SLVs. A ST that appears to have diversified to produce multiple SLVs is called a subgroup founder. In the default setting for the eBURST diagram, a ST with at least two assigned descendent SLVs (i.e. three SLVs in total, as the link from the ST to its putative progenitor is also a SLV) is defined as a subgroup founder. In larger eBURST groups there may be many STs with at least two assigned descendent SLVs, and the number of descendent SLVs that define whether a ST is shown as a subgroup founder should be increased. The STs that are subgroup founders, according to the default definition of a subgroup, or a user-defined definition, are coloured yellow on the eBURST diagram (see examples below). The primary founder of the group is coloured blue. |
サブグループはeBURSTとでは、黄色表示となる。
5. Estimating the level of confidence in the predicted founding ST
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In some cases, particularly in small groups with few SLVs, the predicted primary founder of a group will have little statistical support and a bootstrapping procedure is used in eBURST to provide the level of confidence in the assignment of the primary founder of each group. The bootstrap values are only available using the default group definition as they are not appropriate with less stringent group definitions where an eBURST group may include several unlinked clusters of STs (clonal complexes). |
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eBURST first divides the input population into groups and, for each group, one example of each ST is extracted, and a user-defined (default = 1000) number of random datasets of the same size as the extracted ST set are produced by re-sampling with replacement. For each re-sampling the predicted primary founder is computed, and a tally is kept of the number or times that each ST in the group is predicted to be the primary founder of the group. The bootstrap values shown for each ST are the percentage of times the ST was predicted to be the primary founder of the group in the bootstrap re-samplings. As a ST cannot be the predicted founder if it is not present in a re-sampled dataset, the calculation of the percentage of times each ST is predicted to be the primary founder omits those re-samplings in which that ST is absent. eBURST therefore produces conditional bootstraps, which scale the bootstrap confidence values to 100%; a ST that is the predicted primary founder in every re- sampling in which it is present will have a bootstrap value of 100%. |
次は、PhyloViz:
PhyloViz http://www.phyloviz.net については、
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Data analysis In the current version of PHYLOViZ, you can analyze your data using the several algorithms described below. Press the Right Mouse Button on the Typing Data (now named with the method) and choose compute to access the available analysis algorithms. |