User: biobiu

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biobiu120
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Posts by biobiu

<prev • 45 results • page 1 of 5 • next >
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Predicting peptide binding site of a protein
... Hello, I'm aiming to predict, for a protein of interest, its likelihood to bind a peptide (non-specific peptide, lets assume an optimal peptide exists). Any ideas how to do that? I was thinking to use a tool like [SPRINT-STR][1] but it seems to be offline. The perfect tool will allow me to evaluate ...
peptide written 4 weeks ago by biobiu120
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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 6 months 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 6 months 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 6 months 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 6 months 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 16 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 16 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 16 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 16 months ago by biobiu120 • updated 16 months ago by GenoMax96k
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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 17 months ago by biobiu120

Latest awards to biobiu

Popular Question 6 months ago, created a question with more than 1,000 views. For Does mirna-seq is stranded?
Popular Question 6 months ago, created a question with more than 1,000 views. For realignment of TCGA mirna-sequencing
Popular Question 6 months ago, created a question with more than 1,000 views. For Alignment of targeted sequencing to the whole genome or to targeted reference
Scholar 6 months ago, created an answer that has been accepted. For A: diamond blastp produce longer alignments with lower identity than ncbi blast
Popular Question 15 months ago, created a question with more than 1,000 views. For Does mirna-seq is stranded?
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: miRNA differential expression
Popular Question 22 months ago, created a question with more than 1,000 views. For Does mirna-seq is stranded?
Popular Question 23 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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