Hello,
I am analyzing a set of genomes that our group have sequenced and annotated.
Trying to perform GO enrichment from a set of genes that were observed up and down regulated (from RNA-Seq data), I just find on-line tools that uses model organisms and public genomes as reference or backgroud for GO enrichment.
Does anyone knows a tool that allow me to use my in-house genome sequences for this?
Thanks in advance
Oh, that's indeed a very interesting projects.
My guess is that, you can build some pre-annotation using the sequence similarity to match the gene in your genome with the model organism to give them the fake name, then borrow the GO form the model organism (GO category should be conserved among species during evolution, you may using several model organism to double-check the result)
good luck
Dear Cristina,
Before you do GO Enrichment analysis, you should find out and assign to which GO category your transcripts are belonging, this can be achieved by a blast alignment of your sequences against all the uniprot submitted transcript sequences, which are already GO annotated. On the basis of sequence similarity you can assign the GO terms to your sequences, Once you have this information, you can simply use online software such AgriGO.
In which you have an option of providing your GO dataset by using "Customized Annotation" (http://bioinfo.cau.edu.cn/agriGO/analysis.php). This will perform the enrichment analysis for you.
In place of this as shortcut tool you can also used Blast2GO tool for GO annotation of your transcripts.
Dear Christina,
I´m not pretty sure about the state of your annotations. If all of your gene models have already been annotated with GO-Terms you can use topGO (r-package, https://bioconductor.org/packages/release/bioc/html/topGO.html) to make enrichment analysis.
cheers
Sebastian
Dear Cristina,
You can annotate your gene or protein sequences by first doing a blast alignment of all the sequences to the blast database, and then importing the blast results (.xml format) into Blast2GO (https://www.blast2go.com -- the program is free!). You can run the "mapping" and "annotation" functions in Blast2GO to assign GO terms to each of the genes/proteins that have blast results. It's pretty nice!
Blast2GO can also blast the sequences for you if you import the sequences in fasta format and run the blast function, but the downside is that it will take a very long time to complete. So it's probably better to run the blast step on a computing cluster if you are short on time.
Hope this helps and good luck!
Regards,
Marissa
I agree with Marissa, balst2go is a good option for annotation, however for the enrichment analysis you have either to pay for a blast2go licence or use another software.
Hi Sebastian!
The enrichment analysis (Fisher's Exact Test) should work on the free version of Blast2GO. It just runs VERY slowly in comparison to the PRO version.
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