AiO
by Christiaan Karreman

AiO: a program integrating Oligo ordering/Data Base and DNA/Protein programs.


For technical information click here (document in PDF format - 1 Mb) . And here for the original publication.

AiO (All in One) integrates a number of standalone programs written between 1987 and 2007 by Christiaan Karreman. They vary between programs that were written purely for database (DB) maintenance and graphic programs depicting plasmids or other DNA. The main advantage of the new AiO is the integration of these programs. Oligos can be designed, ordered via EMail and submitted to the various DBs and visualized immediately in a plasmid map, depicting the exact position and orientation of the new oligo.


Just a few of the features of AiO

- Superior Graphics - Plasmid maps, linear maps, virtual agerose gels, flows (family tree of plasmids)
- Alignments, the strategies of which can be saved, edited and added to
- Alignment of the encoded proteins, just give the DNA files and the proteins will be aligned
- Interactive Dotplots, you can zoom in and out and see the sequence behind
- Virtual cloning like you always wanted it, with fragments, PCR products, adaptors TOPO cloning etc
- Create oligo pairs for RT-qPCR fully automatic
- Silent mutagenesis, incorporate restriction sites without changing the protein
- Standard things: translate, restriction sites, DNA editor, digests etc


History

The history of some parts of AiO is rather strange, Dotplot was written in machine code (in a GFA-Basic shell) for the Atari ST (click here for the original publication), ported first to Pascal for VMS/VAX, later to VMS/Alpha. As these OSs became more or less obsolete it was finally ported to Delphi/Windows. I was always curious when I would have to port it to Linux, but I don't think I will have to as AiO will run under Wine.

The maps of the plasmids are drawn using a program that is almost as old as Dotplot. Other parts of the program are newer, some even brand new. AiO is always being extended and improved. Release V7 introduced a graphical interface for virtual cloning; it is just Click and Clone (CnC). Version 8 has been released in 2006 and sported the oligo design subroutine . If you want to see this click here. V9 is still in the making, I know it's been a long time since V8 but I think you'll like the improvements I've made.


How can AiO be used?

AiO was written for workgroups. There might be a number of groups connected to the same server that holds just one copy of the program. It recognizes the various members of the groups and connects them with the group's Data Bases (DBs). Every user has his/hers personal oligo DB and collection of DNA/protein files. (S)He is also entitled to use the central DBs of the group (s)he belongs to and the general DBs.


AiO and its DBs

There are a number of DBs that keep AiO in data.
All these DBs have to have their own editor to keep up to date. Most of the time the 'groupmanager' (one or two persons who are resposible for the integrity of the DBs) is responsible for maintenance of the various DBs. However there are some exceptions. One of these is the DB for the restriction enzymes, every month the new enzymes are down loaded via FTP from the NEB site. Another important exception is the program itself, it fetches new versions of itself and data files from the very HTTP site your browsing at the moment.

Some of the DBs, what they are for and how they are managed:

Own Oligos : every user has a own oligo-DB where (s)he can edit/write/delete and download from the group's oligo DB
Group oligo DB: a DB where all oligos of the group are kept, only group manager has EWD privileges
Restriction enzymes DB: ALL restriction enzymes, automatic
Oligo manufacturer DB: your own list of your favorite manufacturers, only group manager has EWD privileges
User DB: all people that use AiO, only group manager has EWD privileges
Structural DNA DB: data for the graphical programs: how to draw what, only group manager has EWD privileges. This DB comes filled with a fair number of entries. Things like most marker genes and origins of replication are there already. Off course, you can edit/delete/add this DB to make it just perfect.
group manager DB: who is the group manager of which group, only group manager has EWD privileges (once)
Amino acid scoring DB: data for comparisons, everybody has EWD privileges


AiO Details

Implemented at the moment:
GENERAL

Open
Opens DNA/protein files in various formats such as there are: plain text (ASCII), GCG, EMBL and GenBank. All files are opened into a new window with complete editor functions, see below.

New
Opens new empty editor window.

The Editor

Editor functions
	-copy
	-reverse and copy (the clipboard contains a copy of the reversed sequence of your selection)
	-cut
	-reverse and cut (the clipboard contains a copy of the reversed sequence of your selection)
	-paste
	-reverse and paste (think about it)
	-select all
	-delete
	-find (searches upper- and lower- strand, can use restriction enzymes as input)
	-find again
	-reverse
	-uppercase
	-set selection start
	-set selection end
	-show EMBL/GCG/GenBank data
	It also has the following general settings
	-begin: determines the begin of the part of the sequence that the program should work with
	-end: determines the end of the part of the sequence that the program should work with
	-rebuild: reorders the sequence after editing AND the corresponding 'action windows'
	-circular: in case of DNA it is a plasmid!
	-linear
	-selection of restriction enzymes, own oligos, groups oligos or certain combinations.
	-width: output 60 - 100/120

DNA/Protein Programs

-Sequence with sites : the selected part of the sequence is shown with numbering and all restriction enzymes/oligos -depending on your choice- shown underneath.
-Coordinates : all selected RE/oligos with the exact position where they cut/hybridize. Also gives PCR tables.
-Frequency : all selected RE/oligos with the number of times they cut/hybridize.
-Plasmid map, shown is the standard map. There is also a custom (select REs and oligos) version. Uses a DB: it is fully automatic!!
-Linear map
-Digest: cuts the DNA with restriction enzymes and calculates the size off the fragments. Can calculate partial cuts! Makes gel pictures just like Triangle.
-Triangle: makes gel pictures of "double cut" series.
-ORF: finds ORFs, different start-codons, different length.
-Translate: translates DNA into protein, prints DNA + selected protein(s) and sites.
-Backtranslate: answers the question: where can I introduce what sites into my DNA without destroying my encoded protein.
-Oligo Design: you can design oligos by hand or fully automatic.
-Dotplot: compares two sequences.
-Align: compares multiple sequences.
-tAlign: translates DNA into protein and aligns the resulting proteins.


DB Programs

-Search the group oligos
-Search the RE DB
-Search EMBL/NCBI Bank on text or on sequence
-Edit own oligos
-Select the REs you want to use. AiO comes with three standard selctions and gives you the oportunity to create a personal one.
-Edit groups oligos
-Edit structural DNA DB
-Edit user DB
-Edit oligo manufacturer DB


Plasmid Family Programs

Flow
With this program you can create plasmid-flowcharts. The example that is connected to this page (screenshot) took me less1 minute to make. You can save the flow and edit it later. The program's representation on the screen is very schematic. The printed version has a very, very high quality. I have linked a PDF file of the print (here), I have enlarged it at 400% so you can see all the details. For a overview set the zoom to 100%. It is also possible to print it to see how good it is (I use a 1200 DPI printer).


Find and Replace
This will solve a problem I had sometimes:
I had this plasmid I was working with for quite some time, the sequence was deduced from published parts. All of sudden some digests were not conform with the sequence. I started sequencing and found the errors. By that time I had at least 15 plasmids that were based upon the original plasmid. I had to change all those sequences as well. I do not like this kind of editing; it is boring and error prone.
So that is what this program is for; you give the old sequence, the new sequence and it will search the whole DNA subdirectories for files with the old sequence. It will ask you if you want to replace the old with the new for every found file. If the old sequence was found more than once in one file you can even replace just one and leave the other instance.


Virtual cloning
with this program you can create new DNA files using those tools you are most familiar with: restriction enzymes, ligase, PCR and a number of other modifying enzymes. Of course you can use the editor for these things but here you can do everything with a graphical interface. The principle is easy: you create a number of fragments and ligate them together. The various fragments can be modified in a number of ways. AiO uses 4 basic fragments:

- those generated by restriction digest
- Topo TA vectors
- PCR fragments
- Adaptors (ds oligos)

With the exception of the Topo vector fragment all these fragments can be modified further. The ends of the adaptors and of the fragments generated with REs can be modified with enzymes like exonucleases, phosphatases, polymerases or nucleotide transferases (the program automatically detects which of the enzymes can use the generated ends as a substrate). The ends of the PCR fragments can also be further modified by applying REs, the ends that are so created can be modified further. AiO checks if the ends of your fragments are compatible, if so you can ligate them. This program automatically generates flow files!!!!!!!!!


Oligo Programs

-new oligo
-Submit to group's DB
-Transfer oligo from group DB to own DB
-Email to manufacturer


Information

-Who is group manager
-Who is system manager
-Change group manager <--- program not just info !!
-download info: when was the last time RE/program was updated, when is this due again.
-Bug report: just drop me a line.
-Homepage: your connection to this.




Has this made you interested? Then go to the Download page or read the Handbook (PDF format).
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