<p>I'd recommend using ClustalX. You include the full length protein in each alignment along with the domain.
The location of the domain from the start of the protein will then be automatically located.
ClustalX gives a nice GUI interface where the location of each amino acid from the start of the protein is numbered making this very easy to do.</p>

CC BY-SA 4.0
2024-07-17T13:27:20.563Z
2024-07-17T13:27:20.563Z
M__
<p>I have this assignment to align sequences from the domains of 5 different proteins. I extracted the domain sequences. I have done the alignment, but I realize I need to number each sequence (since they are not starting from 1). I believe this will help pinpoint the exact locations of the conserved amino acids.  I haven't found this option on the alignment platforms I have been exploring.</p>

<phylogenetics><sequence-annotation><multiple-sequence-alignment>
How can I include the start and end sequence number while doing MSA alignment with any alignment tool like CLUSTALW?
# How can I include the start and end sequence number while doing MSA alignment with any alignment tool like CLUSTALW?

(Asked by: username_0 on 2024-07-17)

I have this assignment to align sequences from the domains of 5 different proteins. I extracted the domain sequences. I have done the alignment, but I realize I need to number each sequence (since they are not starting from 1). I believe this will help pinpoint the exact locations of the conserved amino acids. I haven't found this option on the alignment platforms I have been exploring.

**Tags:** phylogenetics, sequence-annotation, multiple-sequence-alignment

---

## 1 answers

### Answer by username_1 on 2024-07-17. Score: 0 | Accepted answer

I'd recommend using ClustalX. You include the full length protein in each alignment along with the domain.
The location of the domain from the start of the protein will then be automatically located.
ClustalX gives a nice GUI interface where the location of each amino acid from the start of the protein is numbered making this very easy to do.


---

