Thermo Fisher Scientific Sequence Navigator™ Quick start guide

Brand: Thermo Fisher Scientific

Model: Sequence Navigator™

Type: Quick start guide

Quick

Start

Guide to

Sequence

Navigator™

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1. Launch the Sequence Navigator application

You should see a blank worksheet:

2. Add sequences to be aligned. If the sequences were previously processed in Factura

and the Batch Worksheet was saved, use the IMPORT BATCH WORKSHEET command.

Otherwise, use the IMPORT SEQUENCE command. Both commands are under the

SEQUENCES Menu.

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You should now be able to see the sequences in the project:

3. To reverse complement sequences, select the sequences by Shift-Clicking on the

sequence names and then use the REVERSE COMPLEMENT SEQUENCES command

under the SEQUENCE Menu:

Once the sequences have been reverse complemented, the symbol will appear beside

the sequence name.

You should be able to see the sequences in the project:

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4. To begin the alignment, first choose the sequences to be aligned by Shift-Clicking on

the sequence names. If all of the sequences are to be selected, use the -A keys. Then

choose the CLUSTAL command under the ALIGN Menu:

The following menu will appear allowing you to specify the alignment parameters.

Typically, choose the default parameters and then OK to begin the alignment:

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You should see a progress bar showing you the status of the alignment:

Upon completion, you should be able to see the aligned sequences:

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5. To align nearby gaps in a single column, select the sequences using Shift-Click,

highlight the area of interest on one of the sequences, and choose GATHER GAPS in

the EDIT Menu. To delete all the gaps (and any bases) in a single column, choose

DELETE COLUMN

6. An ambiguity sequence can be generated, which identifies differences between

aligned sequences. Select the sequences of interest (Shift-Click), go to the CREATE

SHADOW(S) command under the SEQUENCES Menu, and choose COMPUTE AMBIGUITY

SEQUENCE:

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A new sequence should appear (#9 in this example). Differences between sequences are

denoted by an asterisk (*).

To create a consensus sequence, select the sequences of interest, choose CREATE

SHADOW(S) under the SEQUENCES Menu, then choose COMPUTE CONSENSUS

SEQUENCE. A new consensus sequence should then appear (#10 in this example).

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Sequences may be edited either from the alignment view or directly on the

electropherograms. To view the electropherograms, select the sequences of interest,

highlight the area of interest on one of the sequences, and hold down the OPTION button

on the keyboard while choosing DISPLAY ELECTROPHEROGRAMS under the

SEQUENCES Menu:

By holding down the option button in the step above, a dialog box appears showing the

display options. If several sequences were selected, use the "Tile: half width" option;

otherwise choose "Tile: full width":

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Sequences may now be edited directly on the electropherograms.

To scroll all electropherograms simultaneously, hold down the option button while using

the scroll bar on an individual electropherogram.

To edit a base, highlight the base and type the new base call.

Clicking on a magnifying glass icon and then on the electropherogram allows you to zoom

in and out.

When finished editing, hold down the option key and close one of the electropherogram

windows. A dialog box will appear allowing you to close all of the electropherogram

windows simultaneously.

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8. To export sequences, select the sequences and then choose EXPORT SEQUENCES

from the SEQUENCE Menu. If one of the sequences is a shadow sequence, first choose

FREEZE SHADOWS, then perform the export.

A dialog box should appear asking how you would like the sequence to be exported:

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9. To save an aligned project, choose SAVE LAYOUT from the FILE Menu. The PRINT

commands are also located in this menu.

To exit the project, choose QUIT.

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Thermo Fisher Scientific Sequence Navigator™ Quick start guide

Brand: Thermo Fisher Scientific

Model: Sequence Navigator™

Type: Quick start guide

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