trinotate or blast2go, which performs better?

[Rachel Levin]

What is the best/most complete method to annotate transcriptomes of non-model organisms?

What are the advantages and disadvantages of trinotate and blast2go?

-Rach

[Tiago Hori]

Blast2go used to be a great piece of software. It's main draw back is that the graphic interface is written in Java  and it is super clunky. You can run it from the command line. Why to I say used to be? Because if you want Blast2Go to work properly now, and use the newest version you have to pay for it. There is nothing that blast2go does that you can't do else where with a little work. I personally prefer trinotate, mainly due to its choice of using sqlLite, which makes moving your results around much much easier than if it was MySQL. 

The beauty of Blast2Go is that it was graphical. I don't recommend it if nothing else out of principle.

T.

Sent from my iPhone

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[Rachel Levin]

Yeah, I only was able to get the free blast2go basic. Besides it being clunky, are the results from blast2go basic not as good either?
Is the main difference between the two that trinotate is more user friendly?

-Rach

On Friday, May 1, 2015 at 11:36:28 PM UTC+10, Tiago Hori wrote:

Blast2go used to be a great piece of software. It's main draw back is that the graphic interface is written in Java  and it is super clunky. You can run it from the command line. Why to I say used to be? Because if you want Blast2Go to work properly now, and use the newest version you have to pay for it. There is nothing that blast2go does that you can't do else where with a little work. I personally prefer trinotate, mainly due to its choice of using sqlLite, which makes moving your results around much much easier than if it was MySQL. 

The beauty of Blast2Go is that it was graphical. I don't recommend it if nothing else out of principle.

T.

Sent from my iPhone

On May 1, 2015, at 10:23 AM, Rachel Levin <rachy...@gmail.com> wrote:

What is the best/most complete method to annotate transcriptomes of non-model organisms?

What are the advantages and disadvantages of trinotate and blast2go?

-Rach

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[Rachel Levin]

Yeah, I only was able to get the free blast2go basic. Besides it being clunky, are the results from blast2go basic not as good either?
Is the main difference between the two that trinotate is more user friendly?

-Rach

Rachel A. Levin

University of New South Wales
Ph.D. Candidate | Centre for Marine Bio-Innovation
School of Biological, Earth, and Environmental Sciences
Phone: +61 4 1643 8884
Email: ra...@rachy.com

Homepage: http://www.bees.unsw.edu.au/rachel-levin 

[Tiago Hori]

The results are not different, but you can't use local servers any more. So if you always have super fast internet, it should not be the end of the world, but it can be. It is for me. I always relied on local blast and GO servers to speed things up, especially when you have some 400,000 sequences to blast. 

Blast2Go is more user-friendly, just because it has a graphical interface, but trinotate will allow you to install the databases locally, which for me is a huge difference. Also, trinotate is open and free. It requires a little more work and I have had to write the odd perl script to deal with outputs, but I prefer it.

T.

Ultimate stresses sportsmanship and fair play. Competitive play is encouraged, but NEVER AT THE EXPENSE OF RESPECT BETWEEN PLAYERS, adherence to the rules and the BASIC JOY OF PLAY.

[Brian Haas]

Trinotate and TrinotateWeb aim to bring together transcript-based ORF prediction, homology searches, functional categories, and expression data together into a simple and intuitive interface.   It's not yet published and still has a way to go to incorporate all the features we're aiming for, but it is free, it's useful in its current state, and it continues to gain traction.

I guess we'll need to rethink our plans to migrate over to MySQL from sqlite...  maybe we'll just have to support both.

~b

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Rachel Levin]

For some reason blastx and blastp with uniref90 is taking MUCH longer what with SwissProt. Why might this be?

Because of this my jobscripts running blastx and blastp with uniref have run out of wall time on the HPC cluster I am working on. If I resubmit and run these jobs again, will they pick up from where they left off or start all over again? 

They all created quite large output files that look as I would expect- just incomplete.

-Rach

Rachel A. Levin

University of New South Wales
Ph.D. Candidate | Centre for Marine Bio-Innovation
School of Biological, Earth, and Environmental Sciences
Phone: +61 4 1643 8884
Email: ra...@rachy.com

Homepage: http://www.bees.unsw.edu.au/rachel-levin 

On Fri, May 1, 2015 at 11:36 PM, Tiago Hori <tiag...@me.com> wrote:

[Tiago Hori]

Uniref will take longer if I am not mistaken. My last search took over 48 hours for 500k contigs, but I was working locally and with 4 threads. 

Unfortunately, I am not sure blast can pick up where it stopped. You could look at the ncbi manual for the standalone blast, it used to be called blast plus, but I think the name changed.

You can do preliminary analysis with the swissprot data alone, sometimes the Uniref adds very little in terms of annotation. 

T.

Sent from my iPhone

[Ken Field]

The uniref database is MUCH larger than swissprot so it is not surprising that it takes longer to search. Blast must search through the entire database to determine the best match for each transcript.

It won't automatically pick up where it left off, but you could do so manually. Look in the outfmt6 file to determine which transcripts it has completed. Then remove those from the fasta file and start the search again.

Multithreading helps -- blast searches scale pretty linearly with the number of cpus that you give them.

Ken

Ken Field, Ph.D.

Associate Professor of Biology

Program in Cell Biology/Biochemistry

Bucknell University

Room 203A Biology Building

[Brian Haas]

If you have access to a compute farm (LSF, SGE, SLURM, or PBS), you can consider trying this:

http://hpcgridrunner.github.io/

and via parallel processing across many compute nodes, you can speed things up a lot!

best,

~brian