User: Kumar

gravatar for Kumar
Kumar40
Reputation:
40
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Trusted
Location:
India
Last seen:
1 day, 13 hours ago
Joined:
2 years, 2 months ago
Email:
d*************@gmail.com

Posts by Kumar

<prev • 162 results • page 1 of 17 • next >
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Comment: C: How to extract all gene nucleotide sequences separately from multiple Genbank fi
... 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 Kumar40
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Comment: C: How to parse protein and dna sequences from prokka generated gbk or gff file bas
... Thank you @Mensur Dlakic. ...
written 6 days ago by Kumar40
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Comment: C: How to extract all gene nucleotide sequences separately from multiple Genbank fi
... @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 Kumar40
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Comment: C: How to parse protein sequence from prokka generated gbk or gff file based on loc
... @cpad0112 I have revised my question. Please go through it. ...
written 7 days ago by Kumar40
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How to parse protein and dna sequences from prokka generated gbk or gff file based on locus_tag?
... 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 ...
genome perl python R bash written 7 days ago by Kumar40 • updated 6 days ago by Mensur Dlakic8.9k
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error in Islandviewer4 API.
... 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 ...
software error perl sequence python bioinformatics written 4 weeks ago by Kumar40
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Comment: C: What is the difference between Average Nucleotide Identity (ANI) and blastn anal
... @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 Kumar40
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What is the difference between Average Nucleotide Identity (ANI) and blastn analysis?
... 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 ...
sequence bioinformatics alignment blast written 5 weeks ago by Kumar40
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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 4 months ago by Kumar40 • updated 4 months ago by Joe18k
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How to incorporate outgroup organism for whole genome 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 phylogeny phylogenetics snp alignment written 4 months ago by Kumar40

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?
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 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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