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] > <javascript:>> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> 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.
