User: utkarsh.sood

gravatar for utkarsh.sood
utkarsh.sood30
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 >
1
vote
1
answer
132
views
1
answer
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.sood30 • updated 9 weeks ago by genomax51k
0
votes
0
answers
192
views
0
answers
Comment: C: DNA replication protein on negative strand
... What is this command for? ...
written 4 months ago by utkarsh.sood30
0
votes
0
answers
192
views
0
answers
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.sood30 • updated 4 months ago by Kevin Blighe24k
0
votes
0
answers
288
views
0
answers
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.sood30
0
votes
0
answers
428
views
0
answers
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.sood30
6
votes
1
answer
551
views
5 follow
1
answer
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.sood30 • updated 15 months ago by Pierre Lindenbaum110k
3
votes
1
answer
471
views
1
answer
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.sood30 • updated 23 months ago by WouterDeCoster30k
0
votes
1
answer
1.6k
views
1
answer
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.sood30 • updated 24 months ago by Sej Modha3.1k
0
votes
2
answers
906
views
2
answers
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.sood30
0
votes
2
answers
906
views
2
answers
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.sood30

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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1081 users visited in the last hour