gap penlty

[naama68]

Hi
How can I add a high gap penlty?
(these are only part of MSA I a list of sequences)
I would like the alignment not to start with a gap.
Thanks

[rcedgar]

well, you can set all the HMM parameters, but this sounds like a very bad idea. from the examples you posted, it's clear that the N-terminals of these sequences don't align, there should be a terminal gap. if you disallow terminal gaps, you'll get one or a few letters followed by a long gap and then the block that aligns.

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On Fri, Jun 16, 2023 at 7:43 AM naama68 ***@***.***> wrote: Hi How can I add a high gap penlty? (these are only part of MSA I a list of sequences) I would like the alignment not to start with a gap. Thanks [image: align] <https://user-images.githubusercontent.com/135230583/246449304-9cbb8bd6-02c3-4ca7-9c85-6fcc6314b014.jpg> — Reply to this email directly, view it on GitHub <#61>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4UI7EPSVDKSAAE4KTH53TXLRWJJANCNFSM6AAAAAAZJLNBNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[naama68]

thanks for the reply. I actually had a problem with the pdbs that were input. regards On 17 Jun 2023, at 2:21, Robert Edgar ***@***.***> wrote: well, you can set all the HMM parameters, but this sounds like a very bad idea. from the examples you posted, it's clear that the N-terminals of these sequences don't align, there should be a terminal gap. if you disallow terminal gaps, you'll get one or a few letters followed by a long gap and then the block that aligns.

On Fri, Jun 16, 2023 at 7:43 AM naama68 ***@***.***> wrote: Hi How can I add a high gap penlty? (these are only part of MSA I a list of sequences) I would like the alignment not to start with a gap. Thanks [image: align] <https://user-images.githubusercontent.com/135230583/246449304-9cbb8bd6-02c3-4ca7-9c85-6fcc6314b014.jpg> — Reply to this email directly, view it on GitHub <#61>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4UI7EPSVDKSAAE4KTH53TXLRWJJANCNFSM6AAAAAAZJLNBNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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