Hello, Thanks Jimmy! The user interface will have a page to do this translation with the next release of TPP. Cheers, --Luis
On Thu, Oct 30, 2014 at 12:23 PM, Veronica Mutchler < [email protected]> wrote: > I was hoping that was the case. But interestingly, the file type says NEW > File whereas it says FA File for the starting transcriptome. I was able to > open it in word pad, however, so hopefully it's fine. I'm hoping to try > and search against it this week. Thank you for all your help. I would not > have figured this out otherwise. > > Veronica > > On Thursday, October 30, 2014 11:50:35 AM UTC-4, Jimmy Eng wrote: >> >> Veronica, >> >> The ".new" extension is just the name it gave to the newly created file. >> It has no meaning in itself and it is intended that you re-name the newly >> created file to whatever you wish. That being said, most database search >> tools don't care what the name of your fasta file is, whether it has a >> ".new" extension or any other random extension. >> >> - Jimmy >> >> On Thu, Oct 30, 2014 at 8:31 AM, Veronica Mutchler <[email protected] >> > wrote: >> >>> It worked!!!! Thank you, Jimmy. What is a .new file type? I've never >>> heard of that before. Will it be recognized by the data base search >>> function? >>> >>> Veronica >>> >>> On Friday, October 24, 2014 4:27:44 PM UTC-4, Jimmy Eng wrote: >>>> >>>> The binary is included with the TPP distribution but I don't believe >>>> that you can access it in the TPP's web interface. So you're going to have >>>> to run it in a command prompt. Here's an example set of instructions >>>> that'll hopefully work for you: >>>> >>>> 1. Create a directory named c:\translate >>>> >>>> 2. Put your transcript database in that directory. It needs to be in >>>> the fasta format. >>>> >>>> 3. Copy the program to this c:\translate directory. You'll find the >>>> program at c:\inetpub\tpp-bin\translateDNA2AA-FASTA.exe. Rename it to >>>> simply "translate.exe" to make things easy. >>>> >>>> 4. Bring up a command prompt: Start Menu -> All Programs -> >>>> Accessories -> Command Prompt >>>> >>>> 5. type "cd c:\translate" to go into the directory you created >>>> >>>> 6. assuming your transcript database is named "mydb.fasta", run the >>>> program by typing "translate.exe mydb.fasta". >>>> >>>> If it runs correctly, it will create a new file with a ".new" >>>> extension. In the example above, the file will be named "mydb.fasta.new" >>>> which will contain a 6 frame translation of your transcripts. >>>> >>>> Good luck and feel free to follow-up with any questions/problems. >>>> >>>> - Jimmy >>>> >>>> >>>> On Fri, Oct 24, 2014 at 11:09 AM, <[email protected]> wrote: >>>> >>>>> I need to translate a transcriptome into a proteome. I see in the >>>>> 4.7.1 release notes that the function is added, but I can't find it >>>>> anywhere inside TPP. >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "spctools-discuss" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to [email protected]. >>>>> To post to this group, send email to [email protected]. >>>>> Visit this group at http://groups.google.com/group/spctools-discuss. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> To post to this group, send email to [email protected]. >>> Visit this group at http://groups.google.com/group/spctools-discuss. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
