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Old 08-26-2011, 06:26 AM   #1
byou678
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Question Need ideas about the advantages of Blast2Go

Could anyone can show the advantages of Blast2Go systematically? Such as doing Annotation or Blast on it. Any discussion is greatly welcome. Thanks in advance!
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Old 08-26-2011, 10:15 AM   #2
westerman
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I guess I don't see what you are trying to ask. Blast2Go at its very basic takes your proteins, does a blast search and adds GO terms. You can toss in Annex GO-augmentation, InterProScan, Enzyme codes, KEGG, and GO-slimming into the mix. All of that is "Annotation".

If you are asking if Blast2Go is better than simple Blasting then the answer is, "sure because it does that plus a lot more"

If you are asking if Blast2Go is better than manual annotation from lab benchwork then the answer is, "no way".

If you are asking if Blast2Go is better than Apollo then the answer is, "different niches -- B2Go is per protein, Apollo is genome-wide"
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Old 08-26-2011, 12:53 PM   #3
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Thanks, westerman.
Yes, the question should be clearer: The blast advantages of Blast2GO comparing to other blast ways. And the comparisons between Blast2GO annotation and other annotation ways. Many thanks to the response.


Quote:
Originally Posted by westerman View Post
I guess I don't see what you are trying to ask. Blast2Go at its very basic takes your proteins, does a blast search and adds GO terms. You can toss in Annex GO-augmentation, InterProScan, Enzyme codes, KEGG, and GO-slimming into the mix. All of that is "Annotation".

If you are asking if Blast2Go is better than simple Blasting then the answer is, "sure because it does that plus a lot more"

If you are asking if Blast2Go is better than manual annotation from lab benchwork then the answer is, "no way".

If you are asking if Blast2Go is better than Apollo then the answer is, "different niches -- B2Go is per protein, Apollo is genome-wide"
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Old 08-26-2011, 01:13 PM   #4
westerman
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Well in many ways Blast is Blast. You can't get much more out of no matter which overlaying program you use. As for B2Go the disadvantage is that if you do blast through the GUI then it takes forever with many (50K+) sequences -- basically the program refuses to overload NCBI or other blast servers. On the other hand you can do your blasting outside of B2Go and import the results. The advantage of B2Go vs. normal Blast is that it gives you graphics and files for all of your results. For example I can generate a graph of the 'top blast' hits for all of my contigs.


Handy when you are working with non-model organisms and want to see if what you are sequencing makes sense. Of course there are other programs that do this as well. But B2Go also provides that annotation. Is it any good? That is hard to say without delving into unknowns and comparative studies. But it at least gives a good starting point.
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Old 08-27-2011, 05:11 AM   #5
SES
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Quote:
Originally Posted by westerman View Post
On the other hand you can do your blasting outside of B2Go and import the results. The advantage of B2Go vs. normal Blast is that it gives you graphics and files for all of your results.
One thing I recall is that the format of the results is derived by the authors. That is, the BLAST XML output is not NCBI BLAST XML format. This may or may not matter to you but it's something to keep in mind (if it's still true). I'm not sure if that means you can load NCBI BLAST XML format or not, I can't remember.
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Old 08-27-2011, 10:47 AM   #6
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Quote:
Well in many ways Blast is Blast. You can't get much more out of no matter which overlaying program you use. As for B2Go the disadvantage is that if you do blast through the GUI then it takes forever with many (50K+) sequences -- basically the program refuses to overload NCBI or other blast servers.
If I'm not mistaken, Blast2GO limits sequences to 10,000bps.

Last edited by phoss; 08-27-2011 at 10:50 AM.
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