User: Mensur Dlakic

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Mensur Dlakic6.8k
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http://www.montana.edu...
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Posts by Mensur Dlakic

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Comment: C: How to get all possible alignments from MAFFT or another global aligner
... To actually answer your question, if you are willing to work a bit: there is a toy global alignment program written by Sean Eddy in the supplement of this paper: https://www.nature.com/articles/nbt0704-909 You should be able to modify it such that it outputs alignments that fit your need. ...
written 8 hours ago by Mensur Dlakic6.8k
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Answer: A: How to get all possible alignments from MAFFT or another global aligner
... The first two alignments are equivalent in terms of score, but the third one isn't because the gap is opened twice. Alignment programs are geared towards finding an optimal alignment rather than finding all alignments. It really is wasteful to output all the possible sub-optimal alignments. It may ...
written 8 hours ago by Mensur Dlakic6.8k
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Answer: A: GO and C++
... No, at least when it comes to publicly shared programs. On average I install 1-2 software packages per week, and I needed Go once in the past 5 years. ...
written 12 hours ago by Mensur Dlakic6.8k
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Answer: A: How to count a sequence and cut in the other sequence?
... You could get this done by using the `-nogaps` option of [**trimAl**][1]. [1]: http://trimal.cgenomics.org/use_of_the_command_line_trimal_v1.2 ...
written 14 hours ago by Mensur Dlakic6.8k
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Comment: C: How many PCs should be considered for downstream analyses?
... And my point is that they are not supposed to be arranged in any kind of trajectory that mimics their differentiation pattern. They are supposed to be well separated, which they are with 15 PCs. You are expecting too much from dimensionality reduction if you think that it is going to recapitulate th ...
written 23 hours ago by Mensur Dlakic6.8k
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Comment: C: Batching PSIBLAST calls and obtaining individual PSSMs
... > I still have a small question. I doubt whether the running time of psiblast is reasonable because it only takes about 10 minutes to run psiblast on the NR database on the ncbi website. But why does it tak longer run time in local It is difficult to answer this question properly without knowing ...
written 1 day ago by Mensur Dlakic6.8k
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Comment: C: How many PCs should be considered for downstream analyses?
... > I'm performing UMAP dimreduction on a subset of my data, to see the overall structure. I've noticed that a low number of PCs (5) provide better time point-to-time point clusterization than a higher number of PCs (15). Not sure what you are looking at to come up with this assessment, but the ey ...
written 1 day ago by Mensur Dlakic6.8k
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Comment: C: Batching PSIBLAST calls and obtaining individual PSSMs
... Not sure what you mean by the relationship between the two databases. If you are talking about the size, NR is 318 million sequences right now, while the latest UniRef90 is 116 million sequences. That will translate into major memory and time savings. I have not used NR for at least 10 years, and a ...
written 1 day ago by Mensur Dlakic6.8k
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Comment: C: Bray-Curtis dissimilarity for comparing genomes, how to normalize?
... I suggest you try [**FastANI**][1]. It compares sequences without actual alignment by calculating k-mer similarity, which in most cases is related to sequence identity. The upside for your purposes is that sequences of different lengths can be used. [1]: https://github.com/ParBLiSS/FastANI ...
written 2 days ago by Mensur Dlakic6.8k
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Answer: A: what are the best metagenome assemblers?
... Don't know how one can choose the best assembler, but these two should be a good starting point: - https://github.com/voutcn/megahit - http://cab.spbu.ru/software/spades/ ...
written 2 days ago by Mensur Dlakic6.8k

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Teacher 1 day ago, created an answer with at least 3 up-votes. For C: Read length for metagenomics analysis
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Scholar 4 days ago, created an answer that has been accepted. For A: Prottest output to Raxml input
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