User: utkarsh.sood
utkarsh.sood • 30
- Reputation:
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- India
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- 4 months ago
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- 3 years, 1 month ago
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Posts by utkarsh.sood
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... 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 6 months ago by
utkarsh.sood • 30
• updated
6 months ago by
genomax ♦ 58k
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... What is this command for? ...
written 8 months ago by
utkarsh.sood • 30
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... 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 8 months ago by
utkarsh.sood • 30
• updated
8 months ago by
Kevin Blighe ♦ 32k
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... 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 11 months ago by
utkarsh.sood • 30
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... 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 19 months ago by
utkarsh.sood • 30
6
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5 follow
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... 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 19 months ago by
utkarsh.sood • 30
• updated
19 months ago by
Pierre Lindenbaum ♦ 114k
3
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532
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1
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... 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 2.3 years ago by
utkarsh.sood • 30
• updated
2.3 years ago by
WouterDeCoster ♦ 34k
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... 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 2.3 years ago by
utkarsh.sood • 30
• updated
2.3 years ago by
Sej Modha ♦ 3.8k
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... 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 2.3 years ago by
utkarsh.sood • 30
0
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... Thanks for your help! Do I have to upload 4000 files separately (as each file contain multiple sequence for 1 protein) ?
...
written 2.3 years ago by
utkarsh.sood • 30
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