SEA-PHAGES | Phage Comparative Genomics Lab Manual

Link to this post \| posted 30 Aug, 2021 21:25
afreise	Hi everyone, The comparative genomics lab manual we created at UCLA is now officially a QUBES resource. You can access the lab manual there as well as teaching/implementation notes. https://qubeshub.org/publications/2745/1 Happy analyses, Amanda

Link to this post \| posted 08 Sep, 2021 15:09
kmaclea	Amanda, This is really helpful! Thank you for sharing very much! Kyle – Kyle MacLea Associate Professor, University of New Hampshire at Manchester kyle.maclea@unh.edu +1 603-641-4129

Link to this post \| posted 08 Sep, 2021 17:07
afreise	You are so welcome, Kyle! Let me know if you have any feedback, suggestions, or questions.

Link to this post \| posted 27 Feb, 2024 15:59
mscaldas	Hi everyone! I'm trying to compare genomes that are even on number of genes read on the forward and reverse orientation, with genomes that are mostly read on the forward orientation. Can I use QUBES for this? Any other ideas? Thanks, Martha

Link to this post \| posted 28 Feb, 2024 18:10
cdshaffer	Yes If you are using a Dot plot tool to compare genomes and it checks both strands you are good. In your case, if you have large sections of one genome that are inverted in another genome(an thus on the other strand) this will be seen in the dot plot as long diagonal lines that change the slope from positive to negative. However, the protocols as posted on QUBES uses Gepard (which is really fast) but it only compares the top strand of each sequence. So to look for similarity when you suspect one sequence is inverted, you would need to compare the reverse complement of one of the phage to the normal strand sequence of the other. Other programs like NCBI BLASTN compare both strands (use the "compare two sequences" check box). BLASTn can be quite a bit slower (when dealing with multiple phage sequences, and may fail totally if your sequences are too long), but it you want to look for large scale similarity and you are not sure which strand to look, BLASTn will probably do better. I would do an initial assessment with BLAST on a single genome vs single genome and once I knew which strands to compare I could do the final comparisons in Gepard. Edited 28 Feb, 2024 22:48

Link to this post | posted 28 Feb, 2024 18:10

cdshaffer

Yes If you are using a Dot plot tool to compare genomes and it checks both strands you are good. In your case, if you have large sections of one genome that are inverted in another genome(an thus on the other strand) this will be seen in the dot plot as long diagonal lines that change the slope from positive to negative.

However, the protocols as posted on QUBES uses Gepard (which is really fast) but it only compares the top strand of each sequence. So to look for similarity when you suspect one sequence is inverted, you would need to compare the reverse complement of one of the phage to the normal strand sequence of the other.

Other programs like NCBI BLASTN compare both strands (use the "compare two sequences" check box). BLASTn can be quite a bit slower (when dealing with multiple phage sequences, and may fail totally if your sequences are too long), but it you want to look for large scale similarity and you are not sure which strand to look, BLASTn will probably do better. I would do an initial assessment with BLAST on a single genome vs single genome and once I knew which strands to compare I could do the final comparisons in Gepard.

Edited 28 Feb, 2024 22:48

Link to this post \| posted 28 Feb, 2024 23:12
mscaldas	Thanks for the feedback, cdshaffer!

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Phage Comparative Genomics Lab Manual - QUBES Resource