User: Dineshkumar K
Dineshkumar K • 40
- 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
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6
votes
3
answers
79
views
3
answers
... 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,
> ...
written 10 days ago by
Dineshkumar K • 40
• updated
10 days ago by
Joe ♦ 18k
0
votes
0
answers
86
views
0
answers
... 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 ...
written 13 days ago by
Dineshkumar K • 40
0
votes
2
answers
145
views
2
answers
... 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 K • 40
1
vote
2
answers
145
views
5 follow
2
answers
... 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. ...
written 17 days ago by
Dineshkumar K • 40
• updated
16 days ago by
shelkmike • 280
0
votes
1
answer
206
views
1
answers
... @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 K • 40
0
votes
1
answer
206
views
1
answers
... 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 K • 40
0
votes
1
answer
206
views
1
answers
... @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 K • 40
0
votes
1
answer
206
views
1
answers
... @ 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 K • 40
0
votes
1
answer
206
views
1
answers
... @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 K • 40
0
votes
1
answer
206
views
1
answers
... @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 K • 40
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