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User: utkarsh.sood

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utkarsh.sood • 30
Reputation:
30
Status:
New User
Location:
India
Last seen:
13 hours ago
Joined:
2 years, 9 months ago
Email:
u***********@gmail.com

Posts by utkarsh.sood

<prev • 35 results • page 1 of 4 • next >
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Software for Quality Check of reads
... 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 ...
reads illumina quality check prinseq written 9 weeks ago by utkarsh.sood • 30 • updated 9 weeks ago by genomax ♦ 51k
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Comment: C: DNA replication protein on negative strand
... What is this command for? ...
written 4 months ago by utkarsh.sood • 30
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DNA replication protein on negative strand
... 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 ...
assembly circular genome oric written 4 months ago by utkarsh.sood • 30 • updated 4 months ago by Kevin Blighe ♦ 24k
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Split a 6 MB genome into 6 files of 1Mb each
... 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. ...
1000000 nucleotide sequence split written 7 months ago by utkarsh.sood • 30
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Pipeline for performing dN/dS analysis on 5000 orthologous proteins
... 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 ...
dn/ds orthologous protein pipeline written 15 months ago by utkarsh.sood • 30
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Construct a gene arrow map to show the gene features
... 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 ...
annotation coordinates gene map written 15 months ago by utkarsh.sood • 30 • updated 15 months ago by Pierre Lindenbaum ♦ 110k
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How sense strand is deciphered after sequencing?
... Hello, I have a query that, how sense strand is deciphered after we get the sequence of a bacterial genome sequenced by SMRT? Thanks! ...
sequencing smrt sense strand direct strand written 23 months ago by utkarsh.sood • 30 • updated 23 months ago by WouterDeCoster ♦ 30k
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How to calculate dN/dS values?
... 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 ...
genome dn/ds paml pal2nal written 24 months ago by utkarsh.sood • 30 • updated 24 months ago by Sej Modha ♦ 3.1k
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Comment: C: Muliple sequence alignment for sequences in more than 4000 files
... 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 24 months ago by utkarsh.sood • 30
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Comment: C: Muliple sequence alignment for sequences in more than 4000 files
... Thanks for your help! Do I have to upload 4000 files separately (as each file contain multiple sequence for 1 protein) ? ...
written 24 months ago by utkarsh.sood • 30

Latest awards to utkarsh.sood

Popular Question 18 days ago, created a question with more than 1,000 views. For How to calculate dN/dS values?
Popular Question 7 months ago, created a question with more than 1,000 views. For How to calculate dN/dS values?
Popular Question 7 months ago, created a question with more than 1,000 views. For How to check whether a genome is circular
Popular Question 7 months ago, created a question with more than 1,000 views. For How to predict the function of hypothetical proteins
Popular Question 7 months ago, created a question with more than 1,000 views. For Identify a sequence as plasmid
Popular Question 8 months ago, created a question with more than 1,000 views. For How to calculate dN/dS values?
Popular Question 12 months ago, created a question with more than 1,000 views. For How to calculate dN/dS values?
Popular Question 12 months ago, created a question with more than 1,000 views. For Identify a sequence as plasmid
Popular Question 12 months ago, created a question with more than 1,000 views. For How to know the name of the pathways using KO numbers?
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