User: utkarsh.sood

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utkarsh.sood30
Reputation:
30
Status:
New User
Location:
India
Last seen:
12 months ago
Joined:
3 years, 9 months ago
Email:
u***********@gmail.com

Posts by utkarsh.sood

<prev • 35 results • page 2 of 4 • next >
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Muliple sequence alignment for sequences in more than 4000 files
... Hi, I have more than 4000 files containing orthologous gene clusters in each file from a bacterial community. How can I perform multiple sequence alignment of all the files in fast and efficient manner? Should I use clustal W, if yes how? Thanks! ...
orthologs sequence clustalw written 3.0 years ago by utkarsh.sood30 • updated 3.0 years ago by Rob100
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DnaA and rpmH genes on the complement strand in a complete genomic sequence
... I have a genomic sequence which got assembled into single contig. I annotated it using RAST. The RAST file showed two copies of Chromosomal replication initiation (DnaA) protein, one on the direct strand and other on the complement strand. To identify the origin of replication I searched for the reg ...
dnaa gene complete genome complement strand written 3.0 years ago by utkarsh.sood30
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Annotating Core and Pan genome
... Hello, I have used get_homologues pipeline to predict core and pan genome among a group of bacteria. What will be the best method to annotate around 5000 core genes and 9000 pan genes quickly and efficiently? Thanks! ...
annotation core-pan genome written 3.0 years ago by utkarsh.sood30
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How to know the name of the pathways using KO numbers?
... Hi I have a list of about 2300 Ko numbers. How can I get the map of pathways using these KO numbers in minimum time. Thanks! ...
pathway kegg written 3.1 years ago by utkarsh.sood30 • updated 2.4 years ago by Santiago Montero-Mendieta120
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Remove duplicate protein sequences having different fasta identifiers
... Hello I have 9058 faa files. some are having duplicate protein sequences but with unique different fasta identifiers. How these duplicate sequences can be removed? Thanks! ...
sequence alignment written 3.1 years ago by utkarsh.sood30 • updated 3.1 years ago by Sej Modha4.2k
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Unknown Sequence Type In MLST
... Hello, I am using MLST 1.8 (https://cge.cbs.dtu.dk/services/MLST/) for Sequence type determination. I am getting a four digit number as (e.g. ST_1195) result for one organism and unknown sequence type for another. What is the significance of these results? Thanks ...
sequence type sequence mlst written 3.1 years ago by utkarsh.sood30
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Comment: C: Covergent contig Warning in RAST
... Thank you for your reply. How should I check my contig for overlaps? and should I randomly take 150 or 200 nucleotides before DnaA gene start? ...
written 3.1 years ago by utkarsh.sood30
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Covergent contig Warning in RAST
... Hi! I have a complete bacterial genome assembled in 1 contig. I have manually made the sequence to start with the first nucleotide of the DnaA gene, and uploaded it on RAST for annotations. But after completion of annotation, it is giving a warning of convergent contig. Can you please help me res ...
genome rast smrt convergent contig written 3.1 years ago by utkarsh.sood30 • updated 3.1 years ago by natasha.sernova3.5k
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Why DnaA protein is the first protein in the genebank file?
... why chromosomal replication initiator proteins are marked as the first protein in the genebank of a complete circular DNA ? ...
ncbi written 3.1 years ago by utkarsh.sood30 • updated 3.1 years ago by natasha.sernova3.5k
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List of all the sequenced Plasmid from Pseudomonas aeruginosa
... Hi! From where can I get the list of all the sequenced plasmid from Pseudomonas aeruginosa? Thanks ...
sequence written 3.2 years ago by utkarsh.sood30 • updated 19 months ago by vmicrobio240

Latest awards to utkarsh.sood

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Popular Question 24 months ago, created a question with more than 1,000 views. For How to calculate dN/dS values?
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Popular Question 24 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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