Application on bacteria protein analysis

[swantan]

Hi, I am working on analyzing one of the proteins of Group A Streptococcus, the M protein. Given the diversity of M protein with a lots of insertions and deletions, I wonder if I can apply virulign to get a better alignment for M protein?

Any advice is greatly appreciated.

Thank you!!
Swan

[ktheyss]

hi Swan, i will check your question with the maintainer of the code. best Kristof

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________________________________ Van: Swan Tan ***@***.***> Verzonden: donderdag 9 mei 2024 13:57 Aan: rega-cev/virulign ***@***.***> CC: Subscribed ***@***.***> Onderwerp: [rega-cev/virulign] Application on bacteria protein analysis (Issue #22) Hi, I am working on analyzing one of the proteins of Group A Streptococcus, the M protein. Given the diversity of M protein, I wonder if I can apply virulign to get a codon alignment for M protein? Any advice is greatly appreciated. Thank you!! Swan — Reply to this email directly, view it on GitHub<#22>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABKKZAGHRIPVIAPHIAGT6KTZBNQBJAVCNFSM6AAAAABHOV32GKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4DONJTGU3TCMI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[plibin]

Hi Swan, I’m not an expert in bacterial protein analysis. Can you provide us with some details on the size of the proteins and possible polyproteins that make up this protein? It is just one protein you would like to focus on? I think it would not be impossible to use virulign, but since we do all kind of things to solve frameshifts, maybe it is not the most efficient tool to use in the context of bacterial alignment. Kind regards, Pieter prof. dr. Pieter Libin Assistant Professor Artificial Intelligence lab Vrije Universiteit Brussel ***@***.******@***.***> http://ai.vub.ac.be<http://ai.vub.ac.be/> From: ktheyss ***@***.***> Date: Monday, 13 May 2024 at 15:26 To: rega-cev/virulign ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [rega-cev/virulign] Application on bacteria protein analysis (Issue #22) hi Swan, i will check your question with the maintainer of the code. best Kristof

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________________________________ Van: Swan Tan ***@***.***> Verzonden: donderdag 9 mei 2024 13:57 Aan: rega-cev/virulign ***@***.***> CC: Subscribed ***@***.***> Onderwerp: [rega-cev/virulign] Application on bacteria protein analysis (Issue #22) Hi, I am working on analyzing one of the proteins of Group A Streptococcus, the M protein. Given the diversity of M protein, I wonder if I can apply virulign to get a codon alignment for M protein? Any advice is greatly appreciated. Thank you!! Swan — Reply to this email directly, view it on GitHub<#22>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABKKZAGHRIPVIAPHIAGT6KTZBNQBJAVCNFSM6AAAAABHOV32GKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI4DONJTGU3TCMI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> — Reply to this email directly, view it on GitHub<#22 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABJOXAR33PXOUQHGHI7EBQTZCC5RTAVCNFSM6AAAAABHOV32GKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMBXGU3TONJYGI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[swantan]

Thank you Kristof @ktheyss for connecting me to the programmer.

Hi Pieter,

Thank you for responding to my question!! Very appreciate it. I actually just started learning bacterial protein analysis as well. The protein that I focus on is the M protein, which is the determination of the emm type for Group A Strep. It is about 500ish aa (~1500nt) in length. The issue is this protein is very diverse and has a lot of variation in terms of length due to insertions and deletions. I used the standard alignment tools but I don't get optimal alignment, largely due to the real insertions and deletions between strains. Hence, I thought of exploring further using virulign, which is a codon-based method.

Hope this explains,
Swan

[plibin]

Dear Swan, I believe virulign would indeed allow you to obtain a high-quality alignment. It might take some compute to obtain it, but you can definitely give it a try. To support new pathogens, the easiest way is to create an XML file with annotation of the region of interest. You can find more info on that here: https://github.com/rega-cev/virulign-tutorial, more specifically in the section “Converting Genbank file to XML file”. Let me know if you need assistance with that. Kind regards, Pieter prof. dr. Pieter Libin Assistant Professor Artificial Intelligence lab Vrije Universiteit Brussel ***@***.******@***.***> http://ai.vub.ac.be<http://ai.vub.ac.be/> From: Swan Tan ***@***.***> Date: Thursday, 16 May 2024 at 16:54 To: rega-cev/virulign ***@***.***> Cc: Pieter Libin ***@***.***>, Comment ***@***.***> Subject: Re: [rega-cev/virulign] Application on bacteria protein analysis (Issue #22) Thank you Kristof @ktheyss<https://github.com/ktheyss> for connecting me to the programmer. Hi Pieter, Thank you for responding to my question!! Very appreciate it. I actually just started learning bacterial protein analysis as well. The protein that I focus on is the M protein, which is the determination of the emm type for Group A Strep. It is about 500ish aa (~1500nt) in length. The issue is this protein is very diverse and has a lot of variation in terms of length due to insertions and deletions. I used the standard alignment tools but I don't get optimal alignment, largely due to the real insertions and deletions between strains. Hence, I thought of exploring further using virulign, which is a codon-based method. Hope this explains, Swan — Reply to this email directly, view it on GitHub<#22 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABJOXAX255ARUXDJRP5747DZCTCAVAVCNFSM6AAAAABHOV32GKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJVGQ3DONBXGA>. You are receiving this because you commented.Message ID: ***@***.***>

[swantan]

Hi Pieter,

Thank you for your input and resource! This is super helpful. I will definitely give it a try.

Thanks a lot,
Swan