Body: <p>I have 10 transcripts where I need to do 5 peptide sequence alignments (2 transcripts per alignment). I need to do this in order to indicate which amino acids lead to which domains.</p>
  <p>My questions are two:</p>
  <ol>
  <li><p>Is there a tool I can use from my laptop that aligns peptide sequences? Because results from the clustal omega peptide alignments web service only last two weeks, they're not ideal for replicability in a paper.</p>
  </li>
  <li><p>The ultimate aim is to use those alignments and domain classifications to a project I am writing and I am trying to make it as presentable and scientific as possible. Any suggestions on how to make peptide alignments and annotations on peptide alignments (which indicate protein domains) look presentable for a paper or if a paper has already shown peptide alignments in a presentable way that would be highly appreciated.</p>
  </li>
  </ol>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-05T07:19:14.897Z
Comments.Text: Could you specify what do you mean by peptide, i.e. are we talking about oligopeptides, 5-20 AA, commonly referred to as simply peptides? Or do you mean protein chains. For the former, domain makes no sense, while for the latter, many tools better than Clustal Omega exist (as Omega is for large datasets, most common being [Muscle](https://www.ebi.ac.uk/Tools/msa/muscle/)). About annotations on protein, the term features is used and there are a few feature viewers... So you may want to specify webapp, Python or R here.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-10T18:46:19.550Z
Comments.Text: Hi Matteo, thank you for your response. 
  I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain disulfide bridges within class I a1 domain). To do this I need to align the peptide sequences of transcripts of that model organism with transcripts of classical MHC I human genes and see which genes from those transcripts have those structural features. So I am looking for a tool to align and annotate those structural features in a replicable manner
Comments.UserDisplayName: mk894
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-10T18:46:26.977Z
Comments.Text: Additionally if you have any other bioinformatic ideas /computational analyses on how to find classical MHC Class I molecules on an organism which is poorly annotated that would highly appreciated!
Comments.UserDisplayName: mk894
Tags: <phylogenetics>
Title: Alignment tools on desktop for peptide alignment sequence and how to make annotations on alignments look presentable?
ThreadText: # Alignment tools on desktop for peptide alignment sequence and how to make annotations on alignments look presentable?
  
  (Asked by: username_0 on 2021-05-04)
  
  I have 10 transcripts where I need to do 5 peptide sequence alignments (2 transcripts per alignment). I need to do this in order to indicate which amino acids lead to which domains.
  
  My questions are two:
  
  1. Is there a tool I can use from my laptop that aligns peptide sequences? Because results from the clustal omega peptide alignments web service only last two weeks, they're not ideal for replicability in a paper.
  2. The ultimate aim is to use those alignments and domain classifications to a project I am writing and I am trying to make it as presentable and scientific as possible. Any suggestions on how to make peptide alignments and annotations on peptide alignments (which indicate protein domains) look presentable for a paper or if a paper has already shown peptide alignments in a presentable way that would be highly appreciated.
  
  **Tags:** phylogenetics
  
  > **Comments:**
  > **username_1**: Could you specify what do you mean by peptide, i.e. are we talking about oligopeptides, 5-20 AA, commonly referred to as simply peptides? Or do you mean protein chains. For the former, domain makes no sense, while for the latter, many tools better than Clustal Omega exist (as Omega is for large datasets, most common being [Muscle](https://www.ebi.ac.uk/Tools/msa/muscle/)). About annotations on protein, the term features is used and there are a few feature viewers... So you may want to specify webapp, Python or R here.  
  > **username_0**: Hi username_1, thank you for your response.  I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain disulfide bridges within class I a1 domain). To do this I need to align the peptide sequences of transcripts of that model organism with transcripts of classical MHC I human genes and see which genes from those transcripts have those structural features. So I am looking for a tool to align and annotate those structural features in a replicable manner  
  > **username_0**: Additionally if you have any other bioinformatic ideas /computational analyses on how to find classical MHC Class I molecules on an organism which is poorly annotated that would highly appreciated!  
  
  ---
  
  ## 0 answers
  
  