User: utkarsh.sood
utkarsh.sood • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- India
- Last seen:
- 7 months, 1 week ago
- Joined:
- 3 years, 4 months ago
- Email:
- u***********@gmail.com
Posts by utkarsh.sood
<prev
• 35 results •
page 1 of 4 •
next >
1
vote
1
answer
341
views
1
answer
... Hi,
I have reads generated for metagenome sequence using Illumina Miseq paired-end reads with the read length of 250 bp. I want to perform the quality check for the obtained sequence.
Could anyone please let me know the software that can be used? I read about Prinseq standalone version but it has ...
written 9 months ago by
utkarsh.sood • 30
• updated
9 months ago by
genomax ♦ 62k
0
votes
0
answers
294
views
0
answers
... What is this command for? ...
written 12 months ago by
utkarsh.sood • 30
0
votes
0
answers
294
views
0
answers
... Hi, I have a genome in which the chromosomal replication protein is on the negative strand with the following coordinates
Start Stop Strand Annotation
1440641 1438221 - DNA gyrase subunit B (EC 5.99.1.3)
1441747 1440638 - DNA recombination and repair protein RecF
1 ...
written 12 months ago by
utkarsh.sood • 30
• updated
12 months ago by
Kevin Blighe ♦ 37k
0
votes
0
answers
428
views
0
answers
... Hi,
I have a complete genome of 6Mb (6000000 nucleotides)
Want to split it into 6 files having unique fasta identifier.
Please help!
Thanks in advance.
...
written 14 months ago by
utkarsh.sood • 30
0
votes
0
answers
644
views
0
answers
... I have predicted the core genome of a group of organism using get homologues. Now I want to do the dN/dS analysis on all the orthologous protein.
Can anyone please suggest any pipeline that can be used to do dN/dS analysis on around 5000 multifasta files.
Thanks
...
written 22 months ago by
utkarsh.sood • 30
6
votes
1
answer
845
views
5 follow
1
answer
... Hello,
I want to generate a gene arrow map showing all the details like gene features, annotation etc. I have the data in the following format:
start stop strand function
208 885 + Chromosomal replication initiator protein DnaA
1576 1157 - FIG00958722: hypothetical protein
2174 157 ...
written 22 months ago by
utkarsh.sood • 30
• updated
22 months ago by
Pierre Lindenbaum ♦ 117k
3
votes
1
answer
572
views
1
answer
... Hello,
I have a query that, how sense strand is deciphered after we get the sequence of a bacterial genome sequenced by SMRT?
Thanks!
...
written 2.5 years ago by
utkarsh.sood • 30
• updated
2.5 years ago by
WouterDeCoster ♦ 36k
0
votes
1
answer
2.1k
views
1
answer
... Hello,
I have made a codon alignment using pal2nal and generated a .codon file. Now I want to calculate the dN/dS values using paml. How can I generate tree file (.tree) and (.cnt) to be used by codeml in paml? If I am doing something wrong please guide me for the correct method to calculate dN/dS ...
written 2.6 years ago by
utkarsh.sood • 30
• updated
2.6 years ago by
Sej Modha ♦ 4.0k
0
votes
2
answers
1.2k
views
2
answers
... I have the access to server with 24 cores and 128Gb RAM.Can I create multiple ClustalW alignments for thousands of fasta in a directory.
The input would be: 1.fasta, 2.fasta... 6405.fasta; where a given file commonly contains14 or more proteins.
The output would be:1.aln, 2.aln... 6405.aln ...
written 2.6 years ago by
utkarsh.sood • 30
0
votes
2
answers
1.2k
views
2
answers
... Thanks for your help! Do I have to upload 4000 files separately (as each file contain multiple sequence for 1 protein) ?
...
written 2.6 years ago by
utkarsh.sood • 30
Latest awards to utkarsh.sood
Popular Question
7 months ago,
created a question with more than 1,000 views.
For How to calculate dN/dS values?
Popular Question
14 months ago,
created a question with more than 1,000 views.
For How to calculate dN/dS values?
Popular Question
14 months ago,
created a question with more than 1,000 views.
For How to check whether a genome is circular
Popular Question
14 months ago,
created a question with more than 1,000 views.
For How to predict the function of hypothetical proteins
Popular Question
14 months ago,
created a question with more than 1,000 views.
For Identify a sequence as plasmid
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How to calculate dN/dS values?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For How to calculate dN/dS values?
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Identify a sequence as plasmid
Popular Question
19 months ago,
created a question with more than 1,000 views.
For How to know the name of the pathways using KO numbers?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1287 users visited in the last hour