User: Dineshkumar K

gravatar for Dineshkumar K
Reputation:
40
Status:
New User
Location:
Kasaragod, Kerala, India
Last seen:
6 days, 13 hours ago
Joined:
1 year, 10 months ago
Email:
d*************@gmail.com

Posts by Dineshkumar K

<prev • 154 results • page 1 of 16 • next >
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How to remove fasta headers in a multifasta file and write file name as a fasta header?
... I have fasta file namely `119XCA.fasta` as shown below, >cellulase ATGCTA >gyrase TGATGCT >16s TAGTATG I need to remove all the fasta headers, keep the sequences one by one and need to write file name as a fasta header. The expected outcome is shown below, > ...
gene genome next-gen sequence alignment written 10 days ago by Dineshkumar K40 • updated 10 days ago by Joe18k
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How to incorporate outgroup organism for a SNP based phylogeny?
... I need to construct a species tree for a plant pathogenic bacterial species which contains numerous pathovars in it. Since I have used AMPHORA tool and managed to extract 23 house keeping genes from 216 strains of the same and constructed species tree using RaxML with 100 bootstrap replicates and en ...
genome sequence alignment snp assembly written 13 days ago by Dineshkumar K40
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Comment: C: Anybody knows any stand alone tool/pipeline for Bacterial Gene Ontology (GO) ana
... I regret for the same and I have deleted the cross-post from the concerned community. Thank you for your valuable suggestion. ...
written 13 days ago by Dineshkumar K40
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5 follow
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Anybody knows any stand alone tool/pipeline for Bacterial Gene Ontology (GO) analysis?
... I have annotated amino acid sequences of various strains of particular bacterial species. I would like to carry out `Gene Ontology` analysis for the same. Therefore, could you please suggest me any standalone `GO analysis tool/pipeline`? Thanks in advance. ...
genome bioinformatics sequence tool gene written 17 days ago by Dineshkumar K40 • updated 16 days ago by shelkmike280
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Comment: C: How to generate reverse complement for the fasta sequences specified in the give
... @JC Thank you so much for your time, consideration and help. Now the script works perfectly. Once again thank you. ...
written 23 days ago by Dineshkumar K40
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Comment: C: How to generate reverse complement for the fasta sequences specified in the give
... cor.csv 3.1,15,7 2.1,5,10 1.1,12,3 lake.fasta >1.1 [Pseudomonas] cissicola strain CCUG 18839 contig_0000001 AAGGCCATCAAGGACGT GGATGAGGTCGTCAAG >8.1 [Pseudomonas] cissicola strain CCUG 18839 contig_0000008 ATGCTTAGCTGATGC >20.1 [Pseudomonas] cissi ...
written 23 days ago by Dineshkumar K40
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Comment: C: How to generate reverse complement for the fasta sequences specified in the give
... @JC now my script is given below by adopting changes as you mentioned #!/usr/bin/perl # getFileSeq.pl $ARGV[1] or die "use getFileSeq.pl ... \n"; my $csv_file = shift @ARGV; my @file_list = @ARGV; my %seqs = (); warn "reading CSV file $csv_file\n"; ...
written 23 days ago by Dineshkumar K40
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Comment: C: How to generate reverse complement for the fasta sequences specified in the give
... @ JC. My revised code is shown below. #!/usr/bin/perl # getFileSeq.pl $ARGV[1] or die "use getFileSeq.pl ... \n"; my $csv_file = shift @ARGV; my @file_list = @ARGV; my %seqs = (); warn "reading CSV file $csv_f ...
written 23 days ago by Dineshkumar K40
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Comment: C: How to generate reverse complement for the fasta sequences specified in the give
... @JC As you mentioned I have deleted this `else { $new_seq = substr($seq, $ini-1, $end-$ini); }` while changing the script. Now it works perfectly fine for my test data, which is shown in my question. However, when I use this script for my real data, I am facing a ...
written 23 days ago by Dineshkumar K40
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Comment: C: Reverse complement a fasta sequences based on the coordinates given in csv file?
... @JC The revised script is extracting the sequences `with one less base` for `Contig3,15,7 and Xantho1,12,3` and reverse complementing the extracted sequences, saving as new_. files. I have fixed this small issue by modifying your script like this `$new_seq = substr($seq, $end-1, $ini-$end+1);` But ...
written 23 days ago by Dineshkumar K40

Latest awards to Dineshkumar K

Great Question 14 days ago, created a question with more than 5,000 views. For What is the difference between blastx and tblastn?
Epic Question 7 months ago, created a question with more than 10,000 views. For devtools Installation error in R (version 3.5.3)?
Popular Question 7 months ago, created a question with more than 1,000 views. For devtools Installation error in R (version 3.5.3)?
Popular Question 7 months ago, created a question with more than 1,000 views. For How to extract a sequence from a multi-fasta file based on its position?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to count the length of fasta sequences?
Great Question 11 months ago, created a question with more than 5,000 views. For devtools Installation error in R (version 3.5.3)?
Centurion 11 months ago, created 100 posts.
Popular Question 12 months ago, created a question with more than 1,000 views. For How to count the length of fasta sequences?
Supporter 13 months ago, voted at least 25 times.
Popular Question 16 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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