mtDNA

"A Complete mtDNA Sequence Analyser"

The program comes with a variety of Databases.

To try the program with the:

Basic database Click here

Instructions:

Use the pull-down menus to choose your selected sequences.
The Basic database sequences are named. The other databases have sequences A1, A2, A3, ....

Before a sequence can be compared to the Cambridge Reference Sequence it is necessary to align it.

So, either press AUTO and then RUN, or do it manually .... see below.
- Please note that AUTO is not always successful -

Press See Comments to show the comments for the sequences.

Press any Display number to display the actual sequences.

To save the report, highlight the report and use 'COPY'(ctrl-c)
and 'PASTE'(ctrl-v) the report into any wordprocessor window.

Manual alignment:

This is not difficult and may allow for a more correct alignment.
1. So, trying with any sequence.
2. Use 'RESET' to clear the display.
3. Press '0k' to display bases 1 - 3000.
4 Traverse the window slowly looking for mutations.
5. Find the first one place where the sequence goes out of alignment.
6. By inspection see if an INSERTION or a DELETION is needed.
7. Select a INSERTION or DELETION point and click.
8. Look at the display again and enter any further INSERTION/DELETION.
9. Now move on to '3k' to look at bases 3001 - 6000.
10. And, almost always make a DELETION at 3106.
11. There are relatively fewer INSERTIONS/DELETIONS needed after 6000.
12. Now RUN can be pressed to see if the alignment process is finished.
The display will now show a list of mutations, such as:
A263G 309.C 315.C T678C A750G A1438G G3010A A4769G A8860G C9356T
A15326G T16519C
(3106- is omitted for the list of results)

Now try with another sequence !

RESET can be used at any stage allowing the process to be restarted.
....
Note:
The program only handles INSERTIONS and DELETIONS that are known to it.

To use the program 'offline':

1. Use FILE & SAVE and copy the appropriate webpage to a directory of your choice.
Put each database in a separate directory.
2. Exit your browser.
3. Run the program by clicking on the directory entry 'COMPLETE_MTDNA_ANALYSER.HTM'.
4. Perhaps make shortcuts and use them if wished.
A different shortcut will be needed for each database.

The program has been tested on 'Internet Explorer 5.5' & 'Firefox 1.0'.

To enter your own sequences to the Basic database:

1. Using the program offline, locate the script file 'COMPLETE_MTDNA.JS'.
2. Next OPEN the script file in a wordprocessor such as NOTEPAD.
(I.e. Open a new NOTEPAD window and drag the directory entry to this window)
3. Add your sequences to the database.
........
4. The structure for the database is as follows:

First line ....... var seq = new Array(

<.... any number of sequences with the format below ....>

Last line ....... "eof");

Sequence Format:
There are 4 lines to each entry and the quotes and commas are essential.

A title & comment .................. "Cambridge \nUnchanged",
('\n' - forces a newline).

The sequence itself ............... "GAT ...... GATG",

A haplogroup field ................ "h2",
(unused)

An Insertion/deletion list ........ "309+ 3106- eol",
(used only as a check)

Note:
The actual sequence can be in lower case, upper case or mixed.
No digits, spaces, carriage returns or linefeeds are permitted in a sequence.
'Replace' in WORD can be useful in preparing sequences
- use a ' ' to replace spaces, '^#' to replace digits,
and '^0010' and '^0013' to remove carriage returns & linefeeds.

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2007