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Description:

Read the paper on DNAssist in Bioinformatics
See the book chapter on DNAssist

DNAssist provides an intuitive, single interface within which sequence files are displayed, edited and analyzed. Several editor windows may be open, and the user can work in any one of these windows by simply bringing it to the top. The editor window is similar to a word processor window, and sequences can be entered from the keyboard, selected with the mouse pointer, copied, cut and pasted to and from the clipboard, drag-and-dropped within the same or to other editor windows, and text searches performed. The windows can also be cascaded, tiled or minimized. The user can customize the display in editor windows by selecting the font, font size, and line length. A sequence is analyzed by simply bringing an editor window to the top, and selecting the required analysis from the menu. All analyses can also be performed on a selected region of the sequence in an editor window. Right clicking the mouse will provide a context-sensitive popup menu. This gives the user a convenient shortcut to most menu items. DNAssist also provides a Speedbar with buttons representing common actions. The analyses available on DNAssist include:

The conversion of a DNA sequence between the circular and linear forms
The conversion of DNA to a RNA or a protein sequence
The conversion of RNA to a DNA or a protein sequence
Translating a DNA sequence to the amino acid sequence in one, three or all six frames
Locating open reading frames (ORFs) in a DNA sequence
Locating specific sequence patterns in a sequence (this allows wildcards, mismatches and gaps)
Performing a restriction enzyme analysis with a defined set of enzymes
Performing a DNA promoter analysis with specified transcription factors
Locating strong nucleosome positioning signals in DNA
Performing multiple alignments of DNA, RNA or proteins
Obtaining the molecular weight of a nucleic acid or protein
Obtaining the melting temperature of an oligonucleotide
Calculating the pI of a protein
Calculating the hydrophilic, hydrophobic or antigenic profile of a protein
Obtaining the molar absorption coefficient and E_0.1% of a nucleic acid or a protein
Obtaining the nucleotide or amino acid composition of a nucleic acid or protein

DNAssist brings all these features together into one tightly integrated Windows^® application. This gives the user the freedom to work in the intuitive IEAE of DNAssist like in a Word Processing environment, and have an extensive and powerful battery of analytical features a mouse click away.

The result of an analysis is displayed in a result window and can be printed, saved to disk or copied and pasted into third party applications. Saved or copied results retain the format in which they were displayed. The user can select from a wide range of formatting options. This includes the display of sequences as continuous lines of text or as text blocks. One or both strands of a DNA sequence can be displayed. The position of the sequence numbers relative to the sequence can also be specified, as can the font face and size. The user can also specify the colors of boxes used to indicate identical or conserved amino acids in multiple alignments. It is thus possible to customize DNAssist to the preference of each user. The display formatting options and the editor window options are saved to the registry when the user exits DNAssist. In a multiple user environment, these settings are associated with the name under which the user logged onto Windows®. This allows many users to use DNAssist on a single computer, where each user will have customized preferences that are not changed by those of the other users.