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关 键 词：GPMAW怎样用
行 业：IT 软件 通讯软件
发布时间：2021-12-03
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A17Two sections of the main toolbar are of direct interest to the sequence window, the Control section (described later in Mass calculations) and the Search and cleavage section:
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.
Mass analysis: The protein can be cleaved by automatic methods (e.g. a flexible nomenclature for defining enzyme actions) or manually. The peptides are displayed with a number of parameters (various mass values - mono, ave, charges - Bull&Breese index, HPLC index, pI, charge) and can be further worked upon (e.g. cross-linked, new cleavage).
Peptide mass searches can be performed on any local database in FastA format.
Bioinformatics: A number of graphs can be displayed, hydrophobicity, dot-plot, secondary structure prediction. BLAST searches can be performed on local databases. Multiple alignment using ClustalW.
The CustalW executable is now part of the GPMAw package, but on previous versions you have to install yourself. Read here how.
The ‘Quickcolor’ button (the down-arrow next to the ‘Highlight’ button) opens a menu that enables you to color specific residues with a single click. The choice of selections cannot be changed by the user, but has been chosen to highlight the most common situations (e.g. highlighting R and K for a tryptic digest; C for identifying cross-links etc.).
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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