Genome Explorer short help
Main page description
Two identical panels located above and in the bottom of page, serve for actions on all commands of the session.
Links serve for following operations:
- New session - to create a new session. New session is created in the separate window.
- Clone session - "to clone" current session. Opens to the page, containing true copy of the session. Copies is assigned new identifier.
- Seqman main page - to move to the start page of the program seqman.
- Command window help - to move to the page with instructions to the program.
- Field "Session ID" indicates an identifier of the current session. Identifier is assigned sessions when making automatically or cloning a session.
- Drop down list "Show group" serves for the choice of displayed groups of commands on panels of operations on commands and input of parameters of commands:
- Sequence constructions - to display only commands of the group "sequence constructions".
- Translations - to display only commands of the group "translations".
- Searches - to display only commands of the group "searches".
- All groups - to display commands of all groups.
- Button "Hide all commands" serves for hide all commands of the session. After pressing a button on panels of current operations stays only information on the amount of hiding operations for chosen of the group of commands.
- Button "Unhide all commands" serves for returning in the image of all commands of the session. After pressing a button on panels of current operations are displayed all operations, performed for chosen of the group of commands.
The panel of operations on commands
The panel is organized as the table. The commands are divided on three groups:
- Group "sequence constructions"
- Group "searches"
- Group "translations"
If the part of commands of group is removed from display, after the name of group in brackets it is underlined, how many commands in the given group are not displayed (for example, record " Group 'searches' (14 hidden) " means, that 14 commands of group "searches" are not shown in the table). To display commands of all groups, it is necessary to choose item " all groups " in the list " Show group ".
The line of the table contains parameters for a concrete command. In line are specified:
- N - a serial number of the current command in the group.
- Command - a name of the command.
- Parameters - main parameters of the command.
- Sequence /Sequence I/ File name - an identifier of first input sequence.
- Sequence II - an identifier of second input sequence. If for the command not provided by second input sequences, in the cell is put dash.
- Result sequence - an identifier of the resulting sequence. If for the command not provided by resulting sequences (for instance, for commands of the searching for and translations), in the cell is put dash.
- Modify command/session - opens window "Operations on command", intended for contributing the changes to the sequence of commands in sessions and their parameters.
- Show history - opens page with history of command.
- Show output - opens window "configure output for the command", or immediately executing command, if adjusting an output for it is not required.
"Operations on command" window
The button located in the column "Modify command/session" on panel of operations on commands opens window "Operations on command". Window serve for contributing the changes to operations on commands and group, to which belongs to a given command.
Operations on the current command:
- "Modify command's parameters" - opens a window with the current parameters of a command in which it is possible to change them. If as a result of changes of parameters the resulting sequence of a command varies, it is reflected in commands in which the resulting sequence is input.
- "Insert new command before the current" - opens a page "Insert new command", with which help it is possible to add a new command before current. Structure of page similarly to a structure of the panel of the input of parameters of commands. In lists of a choice of input sequences the sequences received as a result of performance of the previous commands will contain only.
- "Delete the command" - to remove the current command. If the command has been removed, resulting sequence which was input for any commands (in any of groups) for them in columns "Sequence/Sequence I/File name" and "Sequence II" instead of names of sequences there will be signs on a question, and the button " Show history " and " Show output " will disappear.
- "Hide the command" - to hide current command.
Operations on current group of commands:
- "Hide all commands before the current" - to hide all commands, placed before current. After the name of the group the amount of hiding commands in the given group is displayed.
- "Unhide all commands before the current" - to display all commands, placed before current.
- "Delete all commands after the current" - to delete all commands, placed after current.
Note. Starting a command is always form and perform chain of preceding commands. Thereby, changing a command influences upon following commands.
"Configure output for the command" window
The button placed in the column "Show output" on panel of operations on commands opens window "configure output for the command". Window serves for starting the computation and adjusting the parameters of the output of results of performing an operation.
- In the headline of the window specified identifiers of incoming sequences.
- The panel "Style of output" serves for the choice of the type of the resulting sequence:
- "just print sequence" - not to number positions of the sequence.
- "print positions by start of lines" - to put a number at the beginning of each line.
- "print positions by interval" - to number each 10-letters interval (number of the position is put on first, eleventh position and so on).
- The field "Width of output" serves for input of the width of the line of the resulting sequence. For the output of sequences in one line input a zero width of the line.
- Drop down list "Letters for output" serves for the choice a style of letters:
- "upper case" - capses.
- "lower case" - lower case letters
- The button "Run" serves for starting the computations and output of the result.
- The button "Cancel" serves for the refusal of computations.
History of the command
The button placed in the column "Show history" on panel of operations on commands opens the page with the history of the command.
On page under name of command schematically represented all operations, as a result of which performing incoming sequences for given command appear.
Panel of input of parameters of commands
The commands on a panel are divided into three categories:
- Input sequence - commands, serve for load the sequences:
Note. After performing a command "Load" sequence is loaded on the server and is kept there, while command or the whole session will not be removed.
- Single sequence commands - commands, serve for operations with one input sequence:
- Restriction sites
- Motif search
- AA translation
- 2 sequence commands - commands, serve for operations with two input sequences:
- Sequence search
"Sequence", "Sequence I" and "Sequence II" lists serve for the choice of input sequences. Button "Info" opens a page with information on sequence, chosen in the list (FASTA-headline, total amount of letters, amount of A, T, G, C, N and gaps in sequences).
Reference [H] before the name of the command opens a page with the description of the command.
The button "Perform" opens a page, serve for input of parameters of the chosen command.