User: Mensur Dlakic

gravatar for Mensur Dlakic
Mensur Dlakic5.8k
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USA
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http://www.montana.edu...
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Posts by Mensur Dlakic

<prev • 586 results • page 2 of 59 • next >
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Answer: A: How do I download NCBI prokaryote Genbank and RefSeq databases as single flat te
... To the best of my knowledge, what you want to do is not possible. I don't know the exact reason, but I would guess it is because there isn't enough demand among users to download a single flat file with all RefSeq genomes. Most people like to customize their downloads, and most people have no proble ...
written 18 days ago by Mensur Dlakic5.8k
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Comment: C: How do I correctly add chain ID to my pdb file?
... This Perl script could work: http://www.canoz.com/sdh/renamepdbchain_pl.txt ...
written 22 days ago by Mensur Dlakic5.8k
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Answer: A: How do I correctly add chain ID to my pdb file?
... [**Rosetta**][1] suite has a Perl script `addChain.pl` that does just that, but it may be an overkill to download the whole package just for that. It seems that [**pdb-tools**][2] would be a simpler solution. In simple terms, you need to read the file line by line, and put a chain into `column 22` ...
written 22 days ago by Mensur Dlakic5.8k
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Comment: C: makeblastdb undocumented exit code
... Did you try running `blastn` on this database, and if so, did it work? If all worked as expected, everything we are typing here is just an exercise in understanding the idiosyncrasy of Windows error codes. By the way, you didn't give use a true output of your command, as the input command has a dif ...
written 22 days ago by Mensur Dlakic5.8k
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Comment: C: Best practice to find regulatory motifs in a set of sequences
... Still the same advice, except that now the argument is even stronger for not doing it on such a large dataset. At least in prokaryotes one could safely assume that a motif is likely palindromic and at least 10 bp wide, which amounts to a decent signal. Eukaryotic motifs are typically shorter and non ...
written 22 days ago by Mensur Dlakic5.8k
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Answer: A: Best practice to find regulatory motifs in a set of sequences
... This sounds like you are trying to find at once all regulatory motifs in a whole genome, and seems prokaryotic by size. That can't be done because there will not be enough statistical support for whatever is found, and it may not be tractable in terms of time. Even if I am wrong in my guess regardin ...
written 22 days ago by Mensur Dlakic5.8k
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Comment: C: bias introduce during metagenome binning due to random amplification prior to li
... To your point (A), you could be right. Still, assembling the reads is still by far the cheapest step - both in terms of time and money - compared to all the steps they must have done so far. The point is to get the information, however biased and incomplete it may be. Which brings me to your point ( ...
written 23 days ago by Mensur Dlakic5.8k
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Comment: C: bias introduce during metagenome binning due to random amplification prior to li
... I am curious why you wouldn't bother assembling. Other than spending some energy to run a computer - which may be running anyway - what is the downside? The poster has already said that "the starting material is extremely difficult to obtain and has a very low amount of biological matter" so they pr ...
written 23 days ago by Mensur Dlakic5.8k
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Answer: A: bias introduce during metagenome binning due to random amplification prior to li
... I know of at least couple of binning programs that do not use coverage information for binning: - https://github.com/tetramerFreqs/Binning - http://claczny.github.io/VizBin/ Even for tools that do, like [**CONCOCT**][1], coverage is just one of hundreds of features, so random amplification shoul ...
written 23 days ago by Mensur Dlakic5.8k
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Answer: A: Measuring sequence similarity between draft genomes
... [**FastANI**][1] and [**pyani**][2] will do alignment-free comparisons of whole genomes. [1]: https://github.com/ParBLiSS/FastANI [2]: https://github.com/widdowquinn/pyani ...
written 25 days ago by Mensur Dlakic5.8k

Latest awards to Mensur Dlakic

Appreciated 5 days ago, created a post with more than 5 votes. For A: Multiple alignment software
Scholar 13 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 16 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 16 days ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 21 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 29 days ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 29 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Pundit 4 weeks ago, created a comment with more than 10 votes. For C: A petition to ask the Federal German Government to stop locking away genomic dat
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 6 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 7 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 7 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: PCA cannot separate different breeds
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Scholar 8 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 9 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: PCA cannot separate different breeds
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Performing Hmmer search against pfam versus UniRef100
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For C: PCA cannot separate different breeds
Scholar 10 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 11 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis

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