Closed naama68 closed 1 year ago
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
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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]
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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