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This is the basic working window of GPMAW. Most other windows will be derived from this window and are called daughter windows.
f you copy the sequence to the clipboard (Edit|Copy to clipboard or Ctrl+C), you will only copy any peptide(s) selected. If no part of the sequence is selected, the whole sequence will be copied to the clipboard in the format in which it is displayed (i.e. 1- or 3-letter code).
Note, when copying this way, only the sequence and not the name will be copied. Pressing Ctrl+F you will copy the sequence in FastA format (i.e. 1-letter code including the name of the sequence). If you want to copy the complete protein information or if you want to format the sequence (e.g. for a report), you should use the File|Export sequence menu option.
This shows a GPMAW sequence library files containing multiple sequences. As a sequence file is limited to a size of 264000 bytes (characters), there is a limit to the number of sequences that can be stored in a single library. In the present library, ‘blood.seq’, you can see (status bar at the bottom) that the file is 9% filled.
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)。
Sequence handling: Import of sequences from a number of different formats with direct database search in Entrez and in local databases (FastA format and Swiss-Prot). Sequences can be saved in local files (databases) for future reference.
From the sequence window a large number of actions can be performed. Sequences can be exported in FastA format (either singly or all sequences at once) for easy transfer to other programs.
显示1个或3个字母
平均质量/单同位素质量
固定残留物宽度
带有序列信息的提要栏
显示二硫化物桥、改性残留物等
通过**显示部分序列,您可以轻松获得给定肽的质量。为了便于导航,您可以使用特定颜色的残留物(提供三种不同颜色和下划线)。大多数设置可以很*地在系统设置框中预先设置。
序列窗口形成父窗口,从中可以创建大量派生子窗口:
肽窗口
MS/MS窗口
批量搜索、合成搜索
图表:疏水性、二级结构、电荷与酸碱度、点图、α螺旋轮
肽窗口
肽窗口通常通过自动摘要命令从序列窗口中调用。但是,也有其他方法,如手动或半自动分裂。
Sequence window
The sequence window is the central window of GPMAW and default view of a sequence. From here you can call most of other sequence related functions (either through the menu, the toolbar, or the pop-up menu).
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