Transform
Transform 0.2.2.3.0
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Text and DNA protein sequence analysis.   Free
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Transform is a little utility to record often used DNA text / sequence transformations. It's simple to use:
  • 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
What's New
Version 0.2.2.3.0:
  • Fixed a bug which disabled making complementary sequences
  • Fixed a bug which disabled making inverted sequences
  • Versions for MacOS 9, Win, Linux on my website
Requirements
Intel/PPC, Mac OS X 10.2.8 or later






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Transform User Discussion (Write a Review)
ver. 0.x:
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burypromote

+11
burgen commented on 09 Sep 2009
This is very useful! Thanks for the author. However, when I introduced spaces within sequence, then copy the sequence back to textedit, the spaces are gone, only sequence was pasted in textedit. Please fix this.
[Version 0.11]

1 Reply

burypromote
Private (developer) replied on 16 Sep 2011
Sorry, can't reproduce this. Can you give some more info (maybe contact me directly)?
burypromote

+15
umijin commented on 23 Mar 2007
This is an interesting application, and potentially useful for many molecular biologists who need to do quick tranformations of text files of sequences.

Howver, there doesn't seem to be any documentation, nor any developer website (in MacUpdate), just the developer's email address in the app. Many of the functions seem to be self evident. However, there doesn't seem to be any way of actually opening a text file. You have to cut and paste your sequences into a Transform window in order to manipulate them.

The previous version posted on MacUpdate was Donationware, but the current version is listed as shareware here - and Donationware from within the app. Unfortunately, there doesn't seem to be any clear way to actually donate or pay anything. So...

In any case, this app seems to be a decent text tool, though the developer should consider some sort of brief support documents or site for the app.
[Version 0.10.4]

4 Replies

burypromote

+407
MacUpdate-Lon commented on 23 Mar 2007
The reason there is no developer website listed/linked here is because the developer did not provide that info. All info posted on the MacUpdate product page for this app is provided by the developer and if it is lacking or confusing in any way, the developer is the sole responsible party. Since he gave no wesbite address to us, we can not ascertain the veracity of the information provided on the product page for Transform.
burypromote
Private (developer) replied on 26 Mar 2007
Thanks for the comment - I'll add the ability to open text files in the next version. I hadn't done so before as my work flow is usually: work with sequence in GeneJockey, copy paste into transform, clean up and modify, then copy paste into Excel. I expected the work flow to be similar for most scientists so there would be no real need to open text files as the sequences are stored in the sequence program ...
burypromote
Private (developer) replied on 26 Mar 2007
P.S. It is called shareware instead of donationware as there is no donationware category when you submit a program (it's now a pulldown menue with limited choice)
burypromote

+407
MacUpdate-Lon replied on 26 Mar 2007
If it is a software that is restricted in its usage until a 'donation' is made and a registration received by the user to unlock some previously restricted features, then it would be rightly called a shareware. If it is not restricted in its usage at all, then it is a freeware with a donation requested. We'd like to clear this up for all parties concerned, but we're lacking some info.
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Downloads:1,507
Version Downloads:283
Type:Education : Teaching Tools
License:Free
Date:28 Oct 2011
Platform:PPC 32 / Intel 32 / OS X
Price:Free0.00
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Transform is a little utility to record often used DNA text / sequence transformations. It's simple to use:
  • 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
  • ... and much more (just ignore the bits you don't need)
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 in the Windows version) so it should even run if you are on "managed computers" like we are in our lab


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