Translating nucleotide fasta file to AA

[AndrewRGross]

What can I use to translate a large number of short nucleotides to all AA open reading frames?

I have a 27 GB illumina library in fasta format containing dna nucleotide sequences. I would like to convert the entire file into an AA fasta file containing all open reading frames.

I'm surprised and confused that I haven't found an easy way to do this. There are plenty of online tools, but I can't find a simple script that i can run on a server. I wrote a python script, but its too buggy. Does anyone know of a python script or something on git hub that I can download and run?


Server specs: Ubuntu 12.04, 24 cores, 50 GB of RAM

[Brian Bushnell]

Hmmm, I'm actually writing something to do that. Should be done later today.

[AndrewRGross]

Well that's convenient.

I'm very grateful, Brian.

[GenoMax]

Transeq or Sixpack from EMBOSS should work (http://emboss.open-bio.org/) while you wait for Brian to make his program available.

[SES]

I recommend you use EMBOSS because all of the major translation tables are available for one reason. Also, you can access the methods through the web interface, with EBI's web services (programmatic access), from BioPerl, or through the command line. These programs are well tested so you likely won't find issues. If you do run into any issues, there is a large user base and getting help is easy.

[Brian Bushnell]

Ok, my tool's done and uploaded.

translate6frames.sh in=nucleotides.fa out=acids.fa

It handles fastq I/O also, translating the qualities. And it's very, very fast.

[Victoria Arsedmund]

Hi there.. I am Vicki and am a grad student learning the nuances of bioinformatics. I am looking forward to being an active member of this community.

Cheers,
Vicki

[Victoria Arsedmund]

BBmap

Ok, my tool's done and uploaded.

translate6frames.sh in=nucleotides.fa out=acids.fa

It handles fastq I/O also, translating the qualities. And it's very, very fast.

Ok, this is a great program and screams! I have no issues with it running on FASTA or FASTQ file. However, I received a file from a colleague, but don't quite understand how to convert it to FASTA. In fact, I don't even know what the format of this file is. Can someone help me please? The file came from Sanger ABI 3730.

Here is what a representative header looks like:

TYPE: EST
STATUS: New
Clone#: Treelapse_B_1
CLONE: Passaged_embryonic_stem_cell_FL_01_01_A01-C10B_A01
SEQUENCE:

Any help would be most appreciated.

Cheers,
Vicki

[Brian Bushnell]

Hmmm... I don't recognize it, but if it is a standard output format for that machine, then Life Technologies should have a conversion tool. If there are only a few dozen sequences, you could even convert them to fasta manually.

This program claims to "convert anything to fasta", including a couple of ABI's normal output formats, so perhaps it would work?

http://www.dnabaser.com/help/tools-converters/MultiFASTA%20Builder/index.html

I've never tried it, though.

[Victoria Arsedmund]

translation

Thanks a bunch, Brian. Well, I have 1000s of sequences and, therefore, manual editing is out of the question. I will try the program you have suggested and report back.

[GenoMax]

If actual sequence starts after the SEQUENCE tag in your example then a simple script may be what you need to get the CLONE#/CLONE and the SEQUENCE out of the file and in to a new one.

[Victoria Arsedmund]

Well, I tried the trial version of DNAbaser, but it took for ever (not like your translate6frame.sh) and ultimately didn't do a good job of the conversion. So, I uninstalled it promptly. Ultimately, I got my colleague from Germany to send me a fasta formatted file. Thanks for the tips, however.

[Victoria Arsedmund]

Thanks! I was thinking along these lines, but thought that someone may have already solved this problem.