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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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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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.
Originally posted by westerman View PostI 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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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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Originally posted by westerman View PostOn 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.
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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.Last edited by phoss; 08-27-2011, 10:50 AM.
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