What is it?
I find Excel to be brilliant for making pretty sequences and sequence alignments - however each character needs to be in a separate cell.
So I wrote a little utility to do often used text / sequence transformations
- Insert Tab before / after each character
- Insert Return after each character
- Keep only letters a-Z
- Format in blocks of 3, 10, 50, 100
- Remove leading / trailing / multiple spaces
- Reverse / complement/ invert DNA sequence
- Translate DNA sequence in frame 1 / 2 / 3
- Backtranslate protein into human / E. coli DNA (using the most frequently used codon)
- Convert 3-Letter AminoAcid code into 1-Letter code
- Convert 1-Letter AminoAcid code into 3-Letter code (spaced / tabbed)
- Get protein sequence info
If there are other transformations you'd like just drop me a line.
Please note that this program will run as it is - there is no installation, no files will be put anywhere (registry, system, etc) so it should even run if you are on "managed computers" like we are in our lab (which is a pain in the neck in 99% of all cases - IT support should be there for us, not the other way round)
Transform is donationware:
If you find it useful feel free to surprise me with a donation via PayPal ;-)
A MacOS X version can be downloaded from here
a MacOS 8.5 or 9 version from here
a Win98/Me/2000/XP version from here
and a Linux version from here
- added HTML menu
- added “turn selected text into ordered list”
- added “turn selected text into unordered list”
- Format sequence as FASTA (keep only A-Z, add > as first line)
- backtranslate into degenerate DNA sequence
- added info windows for IUPAC, Amino Acids, Genetic code, Polymerases
Plans for improvements in future versions:
• None yet - feel free to send me some
I'm grateful for suggestions. As my work takes me to different places every few years I've set up a separate hotmail account - you can reach me there even when my address has changed. Please send any suggestions you have to
Questions & Answers:
Q: I found a bug!
Then please report it. I do my best to fix bugs as quickly as possible (usually within 24-48 h), but I can't do it if I don't know about it. And that was not a question.
My thanks to the good folks at RealBasic for their powerful and easy to use programming environment. And of course the excellent user community who are there 24/7 for support, advice, and sometimes a shoulder to cry on ;-)
Conditions of use:
You are entitled to download/copy/install/distribute Transform as you see fit. As a matter of fact I positively encourage distribution. Send the original file to you colleagues, friends, students - whomever you think might benefit from it.
Legal mumbo jumbo:
Transform is provided "as is" without warranty of any kind, either expressed or implied. The entire risk arising out of use or performance of Transform remains with you.