User: Dineshkumar K

gravatar for Dineshkumar K
Reputation:
30
Status:
New User
Location:
Kasaragod, Kerala, India
Last seen:
5 days, 17 hours ago
Joined:
11 months, 1 week ago
Email:
d*************@gmail.com

Posts by Dineshkumar K

<prev • 105 results • page 1 of 11 • next >
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Comment: C: Is there any tool available for sequence alignment concatenation and supermatrix
... @h.mon, Yes, I have different length sequences in my gene1.fasta file. Can't I concatenated different length alignment file?. Moreover, I have more than 2000 alignment files, so manual curation is tedious to do. Therefore, could you please suggest any other tool, which can serve my purpose. ...
written 7 days ago by Dineshkumar K30
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Is there any tool available for sequence alignment concatenation and supermatrix file generation other than Fastconcat-G?
... I am trying to concatenate `mafft` and `gblock` processed multiple gene alignment files/sequences and make `supermatrix` by using `FASconCAT-G v1.0`, However, I end up with an error as follows, !FILE-ERROR!: Unequal sequence lengths in file gene1.fasta! READ IN gene1.fasta Is there any way to ...
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Comment: C: Extract sequences consecutively from a large fasta files and save in new fasta f
... Thank you so much `@cpad0112` and @russhh. It works awesome. I ran the following command, ga@pls:~/Desktop/int/tolc$ parallel './seqkit range -r {}:{} *.fasta -o output/group_{}.fasta' ::: $(seq 1 $(grep -c ">" species1.fasta)) and successfully got results in the output folder, The output i ...
written 7 days ago by Dineshkumar K30
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Comment: C: Extract sequences consecutively from a large fasta files and save in new fasta f
... Thank you @Joe, It serve my purpose perfectly. ...
written 7 days ago by Dineshkumar K30
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Comment: C: Extract sequences consecutively from a large fasta files and save in new fasta f
... @ cpad0112 I created a `output` folder and then ran the command as you mentioned, but there is no file has been created in `output` directory. The terminal printed as follows, ga@pls:~/Desktop/int/tolc$ parallel --dry-run 'seqkit range -r {}:{} *.fasta -o output/group_{}.fasta' ::: $(seq 1 $(gr ...
written 8 days ago by Dineshkumar K30
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Comment: C: Extract sequences consecutively from a large fasta files and save in new fasta f
... Thank you russhh, for your suggestion. I would try to do the same. ...
written 8 days ago by Dineshkumar K30
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Comment: C: Extract sequences consecutively from a large fasta files and save in new fasta f
... Thank you @cpad0112. However, it shows error as follows, ga@pls:~/Documents/data/xap95/ortho_cluster/orthogenes_dna/test$./seqkit range -r {}:{} *.fasta -o output/group_{}.fasta ::: $(seq 1 $(grep -c ">" species1.fasta)) [ERRO] invalid range: {}:{}. type "seqkit range -h" for more examp ...
written 8 days ago by Dineshkumar K30
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Comment: C: Need help in programming?
... @russhh, Yes, I have the same number of sequences in the two fasta file ( In reality, I have 30 fasta files and each fasta file consist of 3000 sequences in it. I need to extract position wise 1,2,3...3000 sequences from all the 30 fasta file and save in new files like group1.fasta, group2.fasta.... ...
written 8 days ago by Dineshkumar K30
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Extract sequences consecutively from a large fasta files and save in new fasta files
... I would like to extract sequences consecutively from a large fasta files and save in new fasta files. For example, I have two fasta files namely species1.fasta and species2.fasta as given below, species1.fasta >tag1 TGCAAGAG >amylase ATCGAGAT species2.fasta > ...
perl python R shell fasta written 8 days ago by Dineshkumar K30 • updated 6 days ago by Chirag Parsania1.7k
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Comment: C: How to mine plant-inducible promoter (PIP) box from Xanthomonas genus genome?
... Thank you genomax, ...
written 26 days ago by Dineshkumar K30

Latest awards to Dineshkumar K

Great Question 8 days ago, created a question with more than 5,000 views. For devtools Installation error in R (version 3.5.3)?
Centurion 8 days ago, created 100 posts.
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to count the length of fasta sequences?
Supporter 7 weeks ago, voted at least 25 times.
Popular Question 4 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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