User: Mensur Dlakic

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Mensur Dlakic2.1k
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USA
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http://www.montana.edu...
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14 minutes ago
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4 months, 3 weeks ago
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Posts by Mensur Dlakic

<prev • 217 results • page 1 of 22 • next >
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Answer: A: What are the COG families for these CDs
... Go to [**conserved domains search**][1], paste your sequences, and select "COG" from the "Search against database" drop-down menu. [1]: https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi ...
written 5 hours ago by Mensur Dlakic2.1k
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Answer: A: Question: Is there any software for finding or generating a small peptide ligand
... This kind of predictive work has not been done with much success, especially not in a way that you propose. If this were routinely possible, we'd be able to control bacterial toxins, rogue protein kinases, or any other protein for which the crystal structure is available. I'd venture to say that a p ...
written 6 hours ago by Mensur Dlakic2.1k
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Answer: A: Interpreting co-ordinates file
... I don't think it matters much because you have so little sequence matching. Your longest match is less than 1000 bp, and query coverage is well below 1%. Either something went wrong during the comparison, or your queries are not related to the reference sequence. ...
written 5 days ago by Mensur Dlakic2.1k
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Answer: A: Mapping Gene Annotations to COG Classifications
... After Prokka installation, go to the `db/hmm` directory and either: 1) delete or temporarily move all databases except COGs; 2) rename the COG database so that its name is first alphanumerically (say, 1-COG). That way all your genes will have only COG annotation (case 1), or they will be first annot ...
written 5 days ago by Mensur Dlakic2.1k
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Answer: A: HMMER installed with conda: no tutorial folder
... Not sure what conda does, but if everything else fails you can always download the files directly: http://hmmer.org/ There is a prominent button there that says "Download source" and after unpacking there will be a `tutorial` directory. ...
written 6 days ago by Mensur Dlakic2.1k
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Comment: C: Is that my way to build ncbi blast 2.9.0+ correct?
... I would not worry about difference in executable size. There are many reasons why size would be different: computer architecture, compilers, `static` compilation, debugging options, stripping after compilation. The whole point of running a configuration process is to find a combination of parameters ...
written 6 days ago by Mensur Dlakic2.1k
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Answer: A: Create phylogenetic tree visualization from handful of 16SrRNA .fastq sequences
... Lots of programs for various aspects of molecular phylogeny can be found [**here**][1]. After gathering your 16S rRNA sequences, a step-by-step pipeline would look something like this: 1) align the sequences (I recommend SSU-align, but many people use MUSCLE or other regular alignment programs ...
written 6 days ago by Mensur Dlakic2.1k
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Comment: C: Tool to extract COG information/description
... It is because many proteins are multi-functional. ...
written 7 days ago by Mensur Dlakic2.1k
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Comment: C: running RAxML and MrBayes over concatinated multiple sequence alignments
... My suggestion to you is to find someone who has done this on a scale comparable to yours, and get some ideas about what it takes. Maybe [**this paper**][1] will give you some ideas, though they used only 16 (relatively small) proteins. In my limited experience with large datasets, [**FastTree**][2] ...
written 7 days ago by Mensur Dlakic2.1k
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Answer: A: Software to reconstruct a proteomics-based metabolic pathway
... [**KEGG**][1] should be a good starting point for you. You may need to upload a set of sequences instead of names. [1]: https://www.genome.jp/kegg/ ...
written 7 days ago by Mensur Dlakic2.1k

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