User: Dineshkumar K

gravatar for Dineshkumar K
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

<prev • 86 results • page 1 of 9 • next >
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Comment: C: What is the minimum number/threshold of gaps (NNNNNN) permitted in a draft genom
... Thank you https://www.biostars.org/u/8927/ ...
written 13 days ago by Dineshkumar K10 • updated 13 days ago by ATpoint19k
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What is the minimum number/threshold of gaps (NNNNNN) permitted in a draft genome?
... 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 ...
genome assembly next-gen bioinformatics sequencing written 13 days ago by Dineshkumar K10 • updated 13 days ago by bioexplorer4.2k
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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 K10
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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 K10
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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 K10
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low bootstrap value?
... 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 ...
phylogeny bioinformatics alignment genome written 28 days ago by Dineshkumar K10
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Comment: C: What is the difference between blastx and tblastn?
... Thank you @lieven.sterck for your detailed clarification. ...
written 28 days ago by Dineshkumar K10
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What is the difference between blastx and tblastn?
... 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 ...
ncbi bioinformatics sequence blast assembly written 28 days ago by Dineshkumar K10 • updated 16 days ago by tim.nollan250
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Comment: C: issue with visualising cladogram/phylogenetic tree with multiple sequence alignm
... @SMK, hereafter I would not repeat this mistake. ...
written 29 days ago by Dineshkumar K10
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Comment: C: issue with visualising cladogram/phylogenetic tree with multiple sequence alignm
... @SMK, It works fine. Thank you. ...
written 4 weeks ago by Dineshkumar K10

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Popular Question 20 days ago, created a question with more than 1,000 views. For devtools Installation error in R (version 3.5.3)?

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