0
$\begingroup$

I am running searches for genes using Phaster {PHASTER (PHAge Search Tool Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. } and would like to look up the phages that have them on PhageDB The Actinobacteriophage Database to learn more about their distribution. The blast search returns a lot of information about the phages and I am unsure what part of the sequence it gives for phages would be helpful.

Image

Improve this question
$\endgroup$
5
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Commented Dec 2, 2023 at 0:58
  • $\begingroup$ What is Phaster? Can you please provide a brief description about the program, and ideally a link that we can visit to get more information? Also... this question doesn't really have a question in it. Could you please clarify what more precisely what you are struggling with? $\endgroup$
    – gringer ♦
    Commented Dec 2, 2023 at 8:39
  • $\begingroup$ I am not sure is a good idea to look for result on PHAGEDB , its full name list phagesdb.org/data/?set=all&type=simple , is probably smaller the the hits out of PHASTER $\endgroup$
    – pippo1980
    Commented Dec 3, 2023 at 10:39
  • $\begingroup$ unless I am getting it wrong and you are asking to use phagesdb.org/blast local blast to search for your sequence inside PHAGEDB ? $\endgroup$
    – pippo1980
    Commented Dec 3, 2023 at 10:51
  • $\begingroup$ mmmmmh the phages on PHAGEDB that are not deposited at NCBI are the only one you should look/screen for , but still I am not getting your question PHASTER is used to track leftover presence of phage in plasmid and genomes , PHAGEDB is a repo (kind of non official for actionobacteria phages) or am I wrong ? $\endgroup$
    – pippo1980
    Commented Dec 3, 2023 at 11:00

0

Reset to default

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Browse other questions tagged or ask your own question.