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GPMAW has been prepared for ClustalW since version 6.0. However, due to licencing problems, it has not been possible to include ClustalW in the distribution package, but as the program is freely available for download, its use has been included in GPMAW.
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The coloring of residues is done through a simple edit box (right). Three colors are available (presented in the left-hand column) Setup, and for each color you can have four different entries (max. 10 residues in each entry). Notice that the question mark can substitute for ‘any residue’ (do not use ‘X’ as this is recognized as a specific residue – unknown). If the ‘Highlight global’ check-box is checked, all currently open sequence windows will be colored. If the ‘Keep highlight’ is not checked, the entries will be cleared whenever the ‘Highlight residues’ dialog is accessed.
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The basic unit of most work in GPMAW is a protein sequence. You may choose to enter a sequence manually, load it from a database or directly from the Web (e.g. see B.1/2 and C.1). However, when you work with a sequence on several occasions, you will normally save it to a file on your hard drive. The main advantage to saving sequences locally, in addition to faster access, is that the sequence saved from GPMAW may contain additional information, e.g. modified residues, cross-links, annotations etc. Note that GPMAW sequence libraries may contain multiple sequences. This works in the way that when you save to a file, which already contains one or more sequences, the new one is appended to the file, instead of replacing it.
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序列处理:通过在Entrez和本地数据库(FastA格式和Swiss-Prot)中直接搜索数据库,从许多不同格式的序列中导入序列。序列可以保存在本地(数据库)中,以备将来参考。从序列窗口可以执行大量操作。序列可以以FastA格式导出(单个序列或同时导出所有序列),以便于传输到其他程序。
质量分析:蛋白质可以通过自动方法(如定义酶作用的灵活命名法)或手动方法进行裂解。多肽显示与许多参数(各种质量值- mono, ave,电荷- Bull&Breese指数,HPLC指数,pI,电荷),并可以进一步工作(如交联,新的分裂)。
生物信息学:可显示多种图形、疏水性、点图、二级结构预测。可以在本地数据库上执行BLAST搜索。使用ClustalW的多重对齐。CustalW可执行文件现在是GPMAw包的一部分,但是在以前的版本中,您必须自己安装。
序列窗口
序列窗口是GPMAW的核心窗口并默认显示一个序列。从这里,您可以调用大多数与序列相关的函数(通过菜单、工具栏或弹出菜单)。
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