User: biobiu

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biobiu120
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Posts by biobiu

<prev • 44 results • page 1 of 5 • next >
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Answer: A: diamond blastp produce longer alignments with lower identity than ncbi blast
... See reply of DIAMOND author: http://www.diamondsearch.org/index.php?threads/diamond-blastp-produce-longer-alignments-with-lower-identity-than-ncbi-blast.98/ ...
written 10 weeks ago by biobiu120
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Comment: C: diamond blastp produce longer alignments with lower identity than ncbi blast
... Thanks. Yes I'm using diamond2. I think I'm looking for less sensitive mode (which is not available since I'm using the default- fast mode). But you are probably right- it is worth exploration. ...
written 11 weeks ago by biobiu120
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Comment: C: diamond blastp produce longer alignments with lower identity than ncbi blast
... I've explored the removing the -ungapped flag from blast, it explains some of the difference. Unfortunately I'm try to mimic the blast results (including the ungapped) with diamond. The reason for -xdrop_ungap is unclear to me either (it is hardcoded in a tool I'm using, which I'm trying to replace ...
written 11 weeks ago by biobiu120
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diamond blastp produce longer alignments with lower identity than ncbi blast
... Hi all, I'm using diamond blastp as a (great) alternative for blastp, mainly in order to save time. Although I made efforts to make the alignment with similar parameters as much as possible I find that in most of the cases ncbi blast will prefer smaller alignment length (with higher identity) than ...
alignment diamond blastp written 11 weeks ago by biobiu120
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Categorizing prokka outputs
... I've annotated assembled bins using prokka. Now I want to cluster the genes by function, pathways etc. I thought to categorize enzymes by ec number. Any recommendations on how to do that for non-enzymatic protein coding genes? ...
gene written 12 months ago by biobiu120
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Comment: C: Download EC number tree
... Thanks! The only thing is missing now is the classification of the upper levels (like Class 1 - oxydoreductase) ...
written 12 months ago by biobiu120
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Comment: C: Download EC number tree
... Thanks! I'm not interested in the sequences but in the enzyme annotations. ...
written 12 months ago by biobiu120
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Download EC number tree
... I want to download for the full EC number tree (with all level) and can't find it. My purpose is to assign all levels for a list of enzymes (in example for 1.1.1.1 not just to tell that it alcohol dehydrogenase but also to tell that it is oxidoreductase (class 1), Acting on the CH-OH group of donor ...
gene written 12 months ago by biobiu120 • updated 12 months ago by genomax91k
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Comment: C: Shotgun rarefactions - metagenomics (microbiome), MetaPhlAn2
... Thanks! I'll update... I'm really stuck with rarefying metaphlan2. Well I can subsample reads but it will take forever to subsample different cuttoffs but with repeats it will take forever to re-run metaphlan2. As for the diveristy- observed OTU (species) and shannon can be calculated easily with re ...
written 13 months ago by biobiu120
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Comment: A: Shotgun rarefactions - metagenomics (microbiome), MetaPhlAn2
... Hi, Did you find any solution to this problem? Any suggestion on how to compute diversity with followed by metaphlan2? ...
written 13 months ago by biobiu120

Latest awards to biobiu

Popular Question 11 months ago, created a question with more than 1,000 views. For Does mirna-seq is stranded?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: miRNA differential expression
Popular Question 18 months ago, created a question with more than 1,000 views. For Does mirna-seq is stranded?
Popular Question 19 months ago, created a question with more than 1,000 views. For Uniquly aligned reads by BWA-mem (MAPQ, and XA tag)

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