Softwares for gene annotation

Question

[grayapply2009]

I did de novo assembly with the RNAseq reads and then blast all the assembled sequences. Then I assigned the blasted gene names to each of my assembled sequences and stored them in a fasta file. Now I'd like to do some gene annotation, e.g. functional analysis, enrichment analysis..., and make some graphs.

Which software should I use, blast2go, DAVID or something else? Are there any good free software I can use? Can I use the fasta file as my input or only the gene names are sufficient?

I'm no bioinformaticists. Please help me.

Answer 1

[arnstrm]

Try trinotate. Much better and faster than blast2go.

[grayapply2009]

Is it free?

[arnstrm]

Yes, open source and free!

[k_mer]

Which would be recommended between Trinotate and Annocript?

Answer 2

[vahapel]

You can use Annocript; https://github.com/frankMusacchia/Annocript for functional annotations (BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission). I think that it is one of best free de novo transcriptome annotation tool.

Answer 3

[Antonio R. Franco]

- Blast2Go is one of my favorite.. Go for it

[grayapply2009]

I tried it but it looks like the free version is not that useful. Did you subscribe it?

[Antonio R. Franco]

The free version has everthing you need to get useful data

Answer 4

[h.mon]

There is also Trinotate.

edit: even though they are not new, only recently I found annot8r and Sma3s. I am currently comparing them on some transcriptomes I have.

[arnstrm]

Didn't see your reply! yes, I second this comment.

[grayapply2009]

How about MAKER? Which one is better? MAKER vs Trinotate?

[arnstrm]

Maker is more of a gene predictor than annotator. Once you have all the predictions, you have to use either trinotate/blast2go to attach function to the predictions.

[Morgan S.]

How to you input Maker's output into Blast2GO? I.e. what output file would you use and how would you annotate it in Blast2GO?

Thanks!

[arnstrm]

Once the Maker completes, you run fasta_merge on the datastore to output genome level fasta (predicted proteins and transcripts), you can use the protein fasta file as input for the downstream analysis. Also, Maker also comes with other accessory scripts, where if you have annotation information (blast hits to swissprot, interproscan as tsv file), can be added to the final GFF3 file.

[h.mon]

Both are annotation pipelines, but Maker is a genome annotation pipeline whereas Trinotate is a transcriptomic annotation pipeline. As you are dealing with a de novo transcriptome assembly, you should proceed with Trinotate.

[Juke34]

So, what was your experience on these tools ?

Do they worth to try them ?