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User: Dineshkumar K

gravatar for Dineshkumar K
Reputation:
30
Status:
New User
Location:
Kasaragod, Kerala, India
Last seen:
4 weeks, 1 day ago
Joined:
1 year, 3 months ago
Email:
d*************@gmail.com

Posts by Dineshkumar K

<prev • 126 results • page 1 of 13 • next >
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Is there any tool available to generate ultrametric tree from a rooted phylogenetic tree?
... I need to generate ultrametric tree from a rooted phylogenetic tree. Therefore, please suggest me any tool which can do the same. Many thanks in advance. ...
phylogeny perl python unix R written 8 weeks ago by Dineshkumar K • 30 • updated 8 weeks ago by Brice Sarver • 3.5k
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Comment: C: How to concatenate clustalw aligned fasta sequence?
... Thank you @lieven.sterck for your valuable suggestion. ...
written 8 weeks ago by Dineshkumar K • 30
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Comment: C: How to concatenate clustalw aligned fasta sequence?
... Sorry for my misinterpretation. @shenwei356 suggestion works well. ...
written 8 weeks ago by Dineshkumar K • 30
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Comment: C: How to concatenate clustalw aligned fasta sequence?
... Dear @ lieven.sterck, Here, I showed an example sequence. But, in reality, I have multiple lined fasta file. All the sequences are not in single line. ...
written 8 weeks ago by Dineshkumar K • 30
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Comment: C: How to concatenate clustalw aligned fasta sequence?
... Thank you @shenwei365. It works fine. But, I could not output the result in new file. It shows result in terminal only, when I output the result using this syntax `> c.fasta`, which show following error. ga@pls:~/Documents/data/xap95/amphora_anal/clustal_codon/gblock_withgab/gblock_gapfree/t ...
written 8 weeks ago by Dineshkumar K • 30 • updated 8 weeks ago by shenwei356 ♦ 5.1k
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Comment: C: How to concatenate clustalw aligned fasta sequence?
... Thank you @Fatima, However it shows following error, ga@pls:~/Documents/data/xap95/amphora_anal/clustal_codon/gblock_withgab/gblock_gapfree/test$ hmmbuild a.hmm a.fasta # hmmbuild :: profile HMM construction from multiple sequence alignments # HMMER 3.1b2 (February 2015); http://hmmer. ...
written 8 weeks ago by Dineshkumar K • 30 • updated 8 weeks ago by genomax ♦ 80k
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How to concatenate clustalw aligned fasta sequence?
... I need to concatenate clustalw aligned multifasta alignment file. I have tried many concatenating tools, which is not recognising the gaps `(---)` of the alignment and ultimately end up with error stating that `sequence dissimilar length `. Is there any way to do the same. For example I have align ...
fasta alignment sequence clustalw written 8 weeks ago by Dineshkumar K • 30 • updated 8 weeks ago by shenwei356 ♦ 5.1k
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How to specify codon based multiple sequence alignment in clustalw command line?
... I need to carryout multiple sequence alignment using clustalw command line. I have been using the following command line which works fine. `clustalw -infile=test.fasta -align -type=DNA -score=PERCENT -outfile=clus_test -output=FASTA ` In addition, I need to specify codon base alignment in the comman ...
fasta sequence alignment clustalw gene written 9 weeks ago by Dineshkumar K • 30 • updated 8 weeks ago by lieven.sterck ♦ 7.2k
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Comment: C: How to parse sequences from a gbk file, based on the coordinates specified in gi
... Dear Joe, It is an output of genomic island gbk file obtained from `islandviewer4` web server. It is a complete genome sequence of Xanthomonas citri. My coordinate file as follows, 638483-646063 638483-646063 1137523-1143403 1182782-1250536 [sample gbk file][1] [1]: https:/ ...
written 10 weeks ago by Dineshkumar K • 30
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How to parse sequences from a gbk file, based on the coordinates specified in given file?
... I need to parse sequences from a gbk file based on the coordinates specified in a given file. For which I have tried to use samtools, but it fails to serve my purpose. Kindly suggest me any tool which can be used to parse the same. Thank you ...
perl python bash gbk written 10 weeks ago by Dineshkumar K • 30 • updated 10 weeks ago by vkkodali • 1.9k

Latest awards to Dineshkumar K

Popular Question 4 months ago, created a question with more than 1,000 views. For How to count the length of fasta sequences?
Great Question 4 months ago, created a question with more than 5,000 views. For devtools Installation error in R (version 3.5.3)?
Centurion 4 months ago, created 100 posts.
Popular Question 6 months ago, created a question with more than 1,000 views. For How to count the length of fasta sequences?
Supporter 6 months ago, voted at least 25 times.
Popular Question 9 months ago, created a question with more than 1,000 views. For devtools Installation error in R (version 3.5.3)?
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