Mapping predicted AMPs back to original contigs?

[Alonna Wright]

Hello! 

I'm interested in determining where AMPs are encoded from (bacteria, phage, host, etc). Is it possible to have an output option of the original nucleotide contig that the AMP was detected in, so that I can associate taxonomic classification with AMP predictions? Or just the original contig identifier provided as an output?  For context, I used the "contig" function and would like to stay with my original assemblies for consistency across my analyses. 

Thank you for your time! 

[Alonna Wright]

I also now see that this community is not only for Macrel usage, sorry! My question is related to Macrel outputs

[Luis Pedro Coelho]

Dear Alonna,

If you look at the file `macrel.out.all_orfs.faa` that is generated in the output directory, the sequence headers should allow you to do what you want (if I understood correctly).

There are prodigal headers, so for example

>k77_5_2 # 1984 # 3048 # 1 # ID=2_2;partial=00;start_type=ATG;rbs_motif=TAAAAA;rbs_spacer=7bp;gc_cont=0.487

means contig "k77_5" from positions 1984 to 3048 (in this case, this is not a smORF, but hopefully the point remains). 

Best

Luis

PS: This is more a more general mailing-list for the AMPSphere project, but macrel is a part of that (the only part that is so far completed/published)

Luis Pedro Coelho | Fudan University | http://luispedro.org

https://orcid.org/0000-0002-9280-7885

--

You received this message because you are subscribed to the Google Groups "ampsphere-users" group.

To unsubscribe from this group and stop receiving emails from it, send an email to ampsphere-use...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/ampsphere-users/256baca2-bbbd-46a0-8232-dc045233d3a0n%40googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

[Alonna Wright]

Hi Luis, 

Thank you for your quick response! This definitely makes more sense now, I just couldn't find anywhere in the documentation of what the values in the headers were for this file. Thank you for clarifying. 

Looking forward to the other AMPSphere project components to come!

Best, 

Alonna

[Luis Pedro Coelho]

Great, but this also indicates a lack of good documentation, which we will work on.

Thanks

Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org

https://orcid.org/0000-0002-9280-7885

To view this discussion on the web visit https://groups.google.com/d/msgid/ampsphere-users/5e4dbf90-be13-4dac-a204-42b19660312en%40googlegroups.com.