User: biobiu
biobiu • 120
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Posts by biobiu
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... 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 ...
written 4 weeks ago by
biobiu • 120
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... 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
biobiu • 120
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... 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
biobiu • 120
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... 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
biobiu • 120
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... 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 ...
written 6 months ago by
biobiu • 120
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... 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? ...
written 16 months ago by
biobiu • 120
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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
biobiu • 120
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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
biobiu • 120
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... 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 ...
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... 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
biobiu • 120
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For Does mirna-seq is stranded?
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For realignment of TCGA mirna-sequencing
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For A: diamond blastp produce longer alignments with lower identity than ncbi blast
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15 months ago,
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For Does mirna-seq is stranded?
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For A: miRNA differential expression
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For Does mirna-seq is stranded?
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For Uniquly aligned reads by BWA-mem (MAPQ, and XA tag)
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