How can I find a new gene in contig sequences on NCBI?

Greetings,

I have recently isolated a new E.coli phage and during the assessment of its host range, I discovered that this particular phage was effective against Pseudomonas aureginosa and staphylococcus aureus in wet lab experiments. However, upon examining the complete genome of the phage on NCBI, I noticed that it did not exhibit any similarities with known P. aureuginosa and S. aureus phages. Additionally, when I performed a blastp analysis on all the phage proteins in NCBI, I could not identify any homology with the aforementioned P. aureuginosa and S. aureus phages. Normally, I would expect to observe some degree of homology, especially in proteins responsible for recognition, such as tail proteins or lytic proteins.

My question is how I can determine the wide host range of the phage based on its genome. It appears that bioinformatic tools should provide information regarding the extent of the phage's host range. I would greatly appreciate your comments and recommendations on this matter.

Thank you.

My whole genome sequence submission was returned by NCBI for the following reasons:

1. That the assembly may be

contaminated with sequences from one or more other organism(s)

2. The genome size of your submission falls outside of

the expected size range for the organism specified in your

submission.

Please my respected scholars, what online tool(s) can I use to remove the contaminants from the assembly genome?

Hi everyone! I hope you all are fine. I have tried many tutorials regarding the calculation of alpha and beta diversity, however, my RStudio is throwing up so many issues. Packages aren't getting installed due to some compatibility issues. That's another discussion. However, may I request you all to kindly guide me in calculating these diversity indices?

What R script should I follow to calculate the Alpha and Beta- diversity indices. People have told me to use vegan, but how to go about it?

P.S. My input taxonomic data comes from Kraken2, so I have sample_kraken_report.txt for all my samples.

I upload a genome to check using Busco via galaxy server. Currently, it is 2 days and the result is not finished yet?

Did I miss something or is there is a problem?

Thank you in advanced

I am having bacterial contamination in my phages. Even after filtering my phage at 0.22um after a few months, there is a pellet formation occurring below. What should I do to remove contamination of my phage with bacteria?

How many Km and Vmax values pertain to a bisubstrate reaction? and how many Km and Vmax values pertain to allosteric enzymes?

Any insight will be helpful.

Without using g-MMGBSA or similar kind of offline tool is the any online server for predicting MMGBSA/MMPBSA and calculating Delta G.

I know two that are LARMD and Delphi Web server but except these two is there any other servers?

Please help, Thank you very much.

Sincerely-

Sunzid.