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Forum: Bioinformatics 12-14-2015, 02:31 AM
Replies: 7
Views: 4,008
Posted By sgoetz
Hi Kurban910. Blast2GO...

Hi Kurban910.
Blast2GO (https://www.blast2go.com) should work fine for the functional annotation of an assembled transcriptome. The most time consuming step will be the blasting. You can do this...
Forum: Bioinformatics 11-23-2015, 09:33 AM
Replies: 3
Views: 1,583
Posted By sgoetz
Hi SES. Blast2GO is freely available for...

Hi SES.
Blast2GO is freely available for academics in the basic version. You can register and download it from here: https://www.blast2go.com/blast2go-pro/b2g-register-basic
Its allows NCBI...
Forum: Bioinformatics 11-23-2015, 09:14 AM
Replies: 3
Views: 1,583
Posted By sgoetz
Hi Jacob. Yes, "level" means in this context...

Hi Jacob.
Yes, "level" means in this context the distance (vertices) from a GO term to the root term.
Indeed, the use of levels to summarize information in the Gene Ontology, which is a direct...
Forum: Bioinformatics 10-21-2015, 01:56 AM
Replies: 5
Views: 995
Posted By sgoetz
Blast2GO (https://www.blast2go.com/) will accept...

Blast2GO (https://www.blast2go.com/) will accept your NCBI Blast+ generated XML file for import. You can provide one file of multiple XMLs, multiple files as well as a folder. Blast2GO supports the...
Forum: Bioinformatics 10-20-2015, 10:02 AM
Replies: 2
Views: 1,078
Posted By sgoetz
Hi, some questions which might help. How...

Hi, some questions which might help.

How many sequences got significant (good) blast results? There are several charts in Blast2GO (https://www.blast2go.com) which might help: the amount of hits...
Forum: Bioinformatics 10-13-2015, 03:56 AM
Replies: 1
Views: 2,672
Posted By sgoetz
The gene ontology mapping performance in Blast2GO...

The gene ontology mapping performance in Blast2GO (https://www.blast2go.com) depends and can vary mainly because of three things: The sequence itself, the blast result and the GO database used to do...
Forum: Bioinformatics 09-23-2015, 07:38 AM
Replies: 5
Views: 2,993
Posted By sgoetz
Hi Monika. Just use the "Select by Colour"...

Hi Monika.
Just use the "Select by Colour" function in Blast2GO (https://www.blast2go.com/blast2go-pro/overview) to select sequences by their analysis status.
If you want to select all non-blue...
Forum: General 09-23-2015, 07:04 AM
Replies: 16
Views: 9,892
Posted By sgoetz
A Blast2GO...

A Blast2GO (https://www.blast2go.com/blast2go-pro/download-b2g) User Manual can be found here: https://www.blast2go.com/images/b2g_pdfs/b2g_user_manual.pdf
Forum: General 09-23-2015, 06:59 AM
Replies: 16
Views: 9,892
Posted By sgoetz
If you want to know which sequences...

If you want to know which sequences (transcripts/unigenes/protein) belong to which biological function/gene ontology term with Blast2GO (https://www.blast2go.com/blast2go-pro/overview) you can use...
Forum: Bioinformatics 05-26-2015, 05:52 AM
Replies: 1
Views: 1,039
Posted By sgoetz
Hi Mike. In which format did you save and with...

Hi Mike.
In which format did you save and with which parameters did you run your blast searches? In Blast2GO you can import Blast results as XML. This is possible with the Blast2GO PRO Plugin for...
Forum: Bioinformatics 03-30-2015, 03:47 AM
Replies: 2
Views: 1,674
Posted By sgoetz
Yes, just make sure you have your EST sequences...

Yes, just make sure you have your EST sequences in Fasta format. Load them into Blast2GO and proceed with the steps: NCBI Blast, GO-Mapping, B2G Annotation.

You can also add InterProScan...
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