User: Dineshkumar K
Dineshkumar K • 10
- Reputation:
- 10
- Status:
- New User
- Location:
- Kasaragod, Kerala, India
- Last seen:
- 1 week ago
- Joined:
- 7 months ago
- Email:
- d*************@gmail.com
Posts by Dineshkumar K
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... Thank you https://www.biostars.org/u/8927/ ...
written 13 days ago by
Dineshkumar K • 10
• updated
13 days ago by
ATpoint ♦ 19k
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... I did a bacterial whole genome sequencing by illumina platform. The quality raw reads were subjected for de novo assembly by using [CGE-Bacterial Analysis Pipeline][1] and obtained 4.9 Mb size draft genome, which is closer to the expected genome size of the bacteria. I have subjected my assembled dr ...
written 13 days ago by
Dineshkumar K • 10
• updated
13 days ago by
bioexplorer ♦ 4.2k
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Comment:
C: low bootstrap value?
... @Michael Dondrup,
As I already excluded `gblocks` trimming step, despite end up with the same bootstrap values.
As you mentioned, I would do the individual protein alignment. Anticipated to obtain better bootstrap value. ...
written 27 days ago by
Dineshkumar K • 10
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Comment:
C: low bootstrap value?
... @lieven.sterck,
I have already done with nucleotide sequences, but end up with the same bootstrap values. ...
written 27 days ago by
Dineshkumar K • 10
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Comment:
C: low bootstrap value?
... @jrj.healey,
As you mentioned, all my genomes belongs to the same species, varied by sub species level classification (pathovar). But, one thing I would like to ask you, the tree topology is slightly different from `gyrb and 16s rDNA` based tree of the same. Is it normal? ...
written 27 days ago by
Dineshkumar K • 10
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... Hi all,
I have created a phylogenetic tree (with 500 bootstrap iteration) based on `AMPHORA` [enter link description here][1] tool specified marker genes (28 marker protein sequences were extracted from 30 bacterial genome and concatenated, aligned by `mafft` and trimmed by `gblock server`). Even th ...
written 28 days ago by
Dineshkumar K • 10
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... Thank you @lieven.sterck for your detailed clarification. ...
written 28 days ago by
Dineshkumar K • 10
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... I would like to know exactly, in which aspect blastx and tblasn varies?
As per my understanding, blastx `convert nucleotide to protein and compare with the query protein sequences`
where as, tblastn also does the same thing but, here the query is nucleotide `convert nucleotide to protein and compare ...
written 28 days ago by
Dineshkumar K • 10
• updated
16 days ago by
tim.nollan25 • 0
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... @SMK, hereafter I would not repeat this mistake. ...
written 29 days ago by
Dineshkumar K • 10
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... @SMK, It works fine. Thank you. ...
written 4 weeks ago by
Dineshkumar K • 10
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