User: biobiu
biobiu • 120
- Reputation:
- 120
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 2 months, 1 week ago
- Joined:
- 5 years, 4 months ago
- Email:
- y******@gmail.com
Posts by biobiu
<prev
• 44 results •
page 1 of 5 •
next >
0
votes
2
answers
204
views
2
answers
... 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
biobiu • 120
0
votes
2
answers
204
views
2
answers
... 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
biobiu • 120
0
votes
2
answers
204
views
2
answers
... 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
biobiu • 120
0
votes
2
answers
204
views
2
answers
... 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 11 weeks ago by
biobiu • 120
0
votes
0
answers
214
views
0
answers
... 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 12 months ago by
biobiu • 120
0
votes
1
answer
238
views
1
answers
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
biobiu • 120
0
votes
1
answer
238
views
1
answers
Comment:
C: Download EC number tree
... Thanks!
I'm not interested in the sequences but in the enzyme annotations. ...
written 12 months ago by
biobiu • 120
2
votes
1
answer
238
views
1
answer
... 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 ...
0
votes
1
answer
2.3k
views
1
answers
... 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
biobiu • 120
1
vote
1
answer
2.3k
views
1
answers
... 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
biobiu • 120
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)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1253 users visited in the last hour