User: Kumar
Kumar • 40
- Reputation:
- 40
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- Location:
- India
- Last seen:
- 1 day, 13 hours ago
- Joined:
- 2 years, 2 months ago
- Email:
- d*************@gmail.com
Posts by Kumar
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... Thank you @ cpad0112 I have revised (added `(` after format) your script as you mentioned, however I am getting another error as follows
ga@ga214:~/Documents/data/xap98/gff_gbk_dna_protein/test$ python3 scri.py
Traceback (most recent call last):
File "scri.py", line 13, in
i ...
written 6 days ago by
Kumar • 40
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1
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... Thank you @Mensur Dlakic. ...
written 6 days ago by
Kumar • 40
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... @cpad0112, Please help me to use your script. I mean I have used the command to execute your code as shown below (I have changed my `genbank` file name as `test.gb` as you mentioned in your code and named your python script as `scri.py`),
python3 scri.py
but end up with error as follows,
...
written 6 days ago by
Kumar • 40
0
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1
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... @cpad0112 I have revised my question. Please go through it. ...
written 7 days ago by
Kumar • 40
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... I need to parse `accessory gene sequences (both dna and amino acid sequences)` from `roary pangenome` output. I have the `locus_tag` list and their corresponding `gbk and gff` files, Is there any way to extract both amino acid and dna sequences from the `gbk or gff` files.The `gbk and gff` file were ...
written 7 days ago by
Kumar • 40
• updated
6 days ago by
Mensur Dlakic • 8.9k
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... I have been predicting genomic island using [IslandViewer4][1] batch upload option (HTTP API), I have followed the following command as they mentioned but doing the same, I end up with an error.
```
curl -X POST -H 'x-authtoken:cec7aae4-0189-89ff-9e50-b2a60ff8fef6' -Fref_accnum="NZ_CP009019.1" -Fgen ...
written 4 weeks ago by
Kumar • 40
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1
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... @andres.firrincieli I have used [BPGA][1] pipeline for my analysis, in which output does not have the following files. `accessory gene cluster frequency table (binary matrix 1,0 aka presence,absence)`. In `BPGA` I can obtain `core sequences, accessory sequences and unique sequences` as three individ ...
written 5 weeks ago by
Kumar • 40
2
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1
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... I did the `pan-genome` analysis, from which I got the core, accessory, and unique gene sequences. Now, I need to know specifically which are strains shared more genes among them in the `accessory gene cluster`. Hence, I opted for a strategy, where I firstly extracted all the gene sequences for each ...
written 5 weeks ago by
Kumar • 40
6
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3
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... 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,
> ...
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... 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 4 months ago by
Kumar • 40
Latest awards to Kumar
Popular Question
13 days ago,
created a question with more than 1,000 views.
For How to download multiple sequences from NCBI-Protein or Uniprot databases?
Popular Question
8 weeks ago,
created a question with more than 1,000 views.
For How to download multiple sequences from NCBI-Protein or Uniprot databases?
Great Question
3 months ago,
created a question with more than 5,000 views.
For How to count the length of fasta sequences?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For How to download multiple sequences from NCBI-Protein or Uniprot databases?
Great Question
4 months ago,
created a question with more than 5,000 views.
For What is the difference between blastx and tblastn?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For How to convert Multiple sequence alignment format (fasta, Mega etc.,) to binary MSA fasta format for gene gain and loss analysis in GLOOME server?
Popular Question
6 months ago,
created a question with more than 1,000 views.
For How to convert Multiple sequence alignment format (fasta, Mega etc.,) to binary MSA fasta format for gene gain and loss analysis in GLOOME server?
Epic Question
11 months ago,
created a question with more than 10,000 views.
For devtools Installation error in R (version 3.5.3)?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How to convert Multiple sequence alignment format (fasta, Mega etc.,) to binary MSA fasta format for gene gain and loss analysis in GLOOME server?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How to specify Cut-off/parameters of sequence identity > 70% and query length > 40% in BLAST command line?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For devtools Installation error in R (version 3.5.3)?
Popular Question
11 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
15 months ago,
created a question with more than 1,000 views.
For How to count the length of fasta sequences?
Great Question
15 months ago,
created a question with more than 5,000 views.
For devtools Installation error in R (version 3.5.3)?
Centurion
15 months ago,
created 100 posts.
Popular Question
16 months ago,
created a question with more than 1,000 views.
For How to count the length of fasta sequences?
Supporter
17 months ago,
voted at least 25 times.
Popular Question
20 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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