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Grades Metagenomics report

16 Janeiro 2020, 10:53 Rodrigo Costa

Dear students, The grades for the metagenomics report are now available in the folder "Lectures Rodrigo Costa / Lab Practical". Prof. Miguel will soon integrate these with all the other grades and make them available in the usual "Grades" folder. 

All the best and see you soon. Rodrigo


Elviz 2.0 is back

4 Novembro 2019, 11:14 Rodrigo Costa

For those interested: https://genome.jgi.doe.gov/viz/
Best, 
Rodrigo


Metagenomics report - Deadline extension

4 Novembro 2019, 11:10 Rodrigo Costa

Dear GFC students, 
Hereby I inform that the deadline for handing in your metagenomics report was extended by one week. Take your time to play with antiSmash :)


For those having questions about the exercise, you can find me in the office (room 11-6.11d, South Tower) on Tuesday, Wednesday and Thursday from 10  to 12.
Best wishes, Rodrigo  


Questions - metagenomics report

30 Outubro 2019, 17:58 Rodrigo Costa

Dear all, 

For those wishing to clarify questions and doubts about the metagenomics report, you can find me tomorrow from 10 to 12 am in the office 11-6.11d (South Tower). 
All the best, 
Rodrigo


Metagenomics - Updates and report tips

29 Outubro 2019, 15:29 Rodrigo Costa

Dear all, 

Unfortunately the Elviz website went down last weekend, and currently there is no prediction for when it will become fully functional again. Therefore, those who wished to play with the tool a little more at home will need to wait a bit. 

The Elviz ouput files that you need to use in your report are however available on our webpage. These are the Actinobacteria.fasta and Actinomycetales.fasta files, which you can use to run the jobs needed to search for secondary metabolite biosynthetic gene clusters (BGCs) using antiSmash. 

Several of you have already asked about the fact that you get no results from antiSmash when you run the job with the Actinobacteria.fasta file. That is correct and these are the results you are supposed to get. Try to run the same job now using the "loose" option under "detection strictness" to see what happens (this is not mandatory through, do it just for fun...). The Actinomycetales file will return results on BGCs detected in some of the contigs. These are the ones you need to explore using the antiSmash tools online. 

Moreover, if any team wishes to work with another bacterial group rather than Actinobacteria/Actinomycetales, I´ve uploaded the fasta files containing the contig sequences of the groups Chloroflexi (phylum), Flavobacteria (Class in the phylum Bacteroidetes), Rhizobiales (order in the class Alphaproteobacteria, phylum Proteobacteria), Rhodobacteraceae (family, in the order Rhodobacterales, class Alphaproteobacteria). They all come from the very same metagenome project on Elviz. If you wish to give them a shot using antiSmash and build your report focusing on one of these groups, you´re welcome. 

All the best, 
Rodrigo