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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.
Molar Ext./Abs.@280: Theoretical extinction coefficient / absorption of the protein at 280 nm.
Highlights: Percentage of the sequence, which is inverted (highlighted) or underlined, updated dynamically.
Sel. mass: Mass of the selected (highlighted) part of the sequence. Shown as singly, doubly and triply charged peptide (i.e. residue mass + 18 + charge). Updated dynamically. Note that unlike the peptide mass shown in the toolbar of the sequence window, this is the charged ion. More on peptide selections in part 3.
If you are working with Windows XP you will need to download the file clustalw1.83.XP.zip and decompress this as well. This file expands to a single file called clustalw.exe. Copy this file into the \gpmaw\bin\clustalw\ directory, replacing the file of the same name.
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.
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