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 Sequence Navigator & PAUP

Sequence Navigator Instructions                         PAUP Instructions

HOW TO USE SEQUENCE NAVIGATOR PROGRAM

(Sequence Navigator Program by Applied Biosystems).  This program  allows one to view sequences, edit bases, align different sequences, and create a new sequence (by typing in the sequence from your autorad).

1) under apple menu: click an hold on apple (top-left corner of screen) and drag down and let go at Sequence Navigator

     An untitled spreadsheet appears.

To Type in Sequence from Autorads:

1) under sequence menu: new sequence

2) click O.K. for a new empty DNA sequence

Name your sequence by:

1) click on left I.D. panel (this highlights the area for the name)

2) under sequence menu: set sequence nickname

3) type in the sequence name, then click O.K.

4) under view menu: preferences I.D. panel

5) click on nickname (this will view your name in left I.D.panel)

6) click O.K.

 

To Import your Sequence:

1) under sequence menu: import sequence

2) double-click on a sequence of interest

3) at cursor: type in bases in CAPITAL LETTERS

 

To View Chromatograms (colored peaks):

1) click on name of sequence in left I.D. panel

2) click and hold mouse button down and drag about 20 bases to highlight them (in pink)

3) press apple key and D at the same time to view chromatograms (or under sequence menu: display electropherograms)

(example: if you want to view base #20: highlight from base 10 -30)  The more base you highlight - the smaller the peaks become and the harder to read).

 

To Edit Bases:

1) cut the first few bases and and the end of the sequence where there are a lot of N's

2) place cursor after the base to edit

3) press delete

4) type in base of your choice

 

To View Chromatograms from 2 (or more) Sequences at the Same Time:

1) click on one of the sequence names in left I.D. panel

2) hold shift key down and click on the other sequence name(s)

(This will highlight all sequence names in black)

3) highlight ~20 bases

4) press apple and D together to view all chromatograms

 

To Scroll Down to View Chromatograms Downstream:

                 with the chromatogram panels viewed:

1) click on any one of the chromatogram panels

2) hold option key down and click and hold on the arrow key at bottom left of panel.  (This will scroll both chromatograms at the same time.  You can also view upstream by holding down the option key and     clicking on the arrow to the bottom left of  the panel.)

 

To Get Rid of Chromatogram Panels:

1) click anywhere on the chromatogram panel

2) click on upper left-hand box

 

To Make Spreadsheet Full-Length of Screen:

1) click on upper right-hand box

     ( to make shorter again: click on box again)

 

To align Sequences by a Complete Overlap:

1) highlight all sequence names (remember to hold shift key down when highlighting more than one name)

2) under align menu: clustal

3) click O.K.

 

To Align Sequence by a Partial Overlap:

1) highlight all sequence names (hold shift key down when highlighting)

2) under align menu: overlap

3) click O.K.

 

To Compare 2 Sequences:

1) highlight both sequence names in left I.D. panel

2) under sequence menu: hold mouse key down on create shadows and drag to the right and let go on compare 2 sequences

3) click O.K.

 

The comparison is in between the 2 sequences:

"-" means bases are the same at that site

"*" means bases are different at that site

 

To Make Text Files of Sequences

1) click on sequence name in left I.D. panel

2) under sequence menu: export sequence

3) save as: type in the sequence name

4) click on text (If you leave it on chromatotext, it will not work)

5) make sure the folder you want to save it in is showing at top

6) click on export

 

To Make a Contig:

A contig is a complete sequence of overlapping segments.

 

1) make sure all of the overlapping bases of the 2 sequences are identical to each other

2) highlight the names of the overlapping sequences

3) under sequence menu:

   createshadows compute consenseus sequence

4) the contig appears at the bottom of all of the sequences

5) name the contig:

 

1) click on space in I.D. panel where the name will be

2) under sequence menu: set sequence nickname

3) type in contig name

4) click O.K.

5) under sequence menu: freeze shadow

6) under sequence menu: export sequence

7) make sure your folder name appears at the top

8) save as: type in the contig name

Note:  If you do not export your contig to a folder BEFORE YOU EXIT program, you will not be able to export the contig again when reentering the spreadsheet. 

 

If this happens:1) reopen spreadsheet

2) delete contig sequence by:

3)  click on contig name in I.D. panel

4) under sequences menu: remove sequence

5) remake your contig as described above

 

To Save Layout (spreadsheet):

1) under file menu: save as

2) make sure it is set to your folder

3) type in name of your file

4) click on save

5) check on the hard drive to see if your file was saved in the correct folder

 

To Exit Program:

1) under file menu: quit

2) click on no / no and no more questions

 

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