---
title: "Understanding Peptide Alignment"
slug: "explanation-understanding-alignment"
status: "update"
updated: 2026-10-14T09:23:59Z
published: 2026-10-14T09:23:59Z
canonical: "docs.discngine.com/explanation-understanding-alignment"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://docs.discngine.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Understanding Peptide Alignment

Every peptide SAR Slide is built on an **alignment** — the position-by-position frame that lets Ideation compare peptides of different lengths and compositions. Ideation gives you three ways to get one: **import** it from a file, or compute it with one of two aligners, **center-star** and **PepSeA**. This page explains what an alignment decides, how the three differ, and which one to reach for.

For the step-by-step instructions, see [How to Align Peptides](/public/docs/how-to-align-peptides).

## Why alignment is a choice, not a calculation

Peptides in a series differ in length and composition, so comparing them position-by-position means deciding which monomers "belong" in the same column. There is no single correct answer: pushing two residues into one column asserts they are equivalent, and inserting a gap asserts one peptide is missing something the other has. Every alignment method is a set of trade-offs about which of those assertions to prefer.

The trade-off that matters most in practice is **columns versus honesty**. A narrow frame is easy to read but forces unrelated residues to share positions; a scrupulous frame keeps residues honest but spreads the series across a wide, mostly-empty grid. The three sources below strike that balance differently — and since an alignment belongs to the dataset, you can keep several and compare them.

## The three sources at a glance

|  | **Imported** | **Center-star** | **PepSeA** |
| --- | --- | --- | --- |
| Who decides the columns | You, in a CSV or Excel file | Ideation's own aligner | MAFFT, through the PepSeA service |
| Created at import | No | Yes — *Center-star alignment* | Yes — *PepSeA alignment* |
| How monomers are scored | — | By natural analog and physicochemical family | By the structural similarity of the monomers, from your organisation's monomer similarity matrix |
| Settings you can change | — | None | Alignment strategy and gap penalty |
| Branches | One Excel sheet per branch | Aligned automatically | Aligned automatically |
| Limits | Peptides are matched on their primary identifier | Up to 5,000 peptides, with HELM sequences | Up to 208 distinct non-natural monomers by default |
| Time to get it | Immediate | Quick | Longer: it may wait for the similarity matrix to be rebuilt, and the strategy sets the run time |
| Best for | A curated alignment you already trust | A quick, predictable frame that is easy to reason about | A tighter frame on series rich in non-natural monomers |

Each source shows as a badge on its row in the alignment list — **Imported**, **Center-star** or **PepSeA** — so you always know where an alignment came from.

The method behind each computed source has its own page:

- [Understanding Center-Star Alignment](/public/docs/explanation-understanding-center-star-alignment) — how the centre is chosen, how substitutions are scored, how gap costs are derived.
- [Understanding PepSeA Alignment](/public/docs/explanation-understanding-pepsea-alignment) — the similarity matrix, the monomer limit, and the strategy and gap settings it asks for.

## What you get at import

A peptide dataset is ready to browse as soon as its sequences are parsed. Its alignments are computed **after** that, in the background: every import queues one **center-star** and one **PepSeA** alignment, which appear in the dataset's alignment list and complete on their own. The center-star one usually finishes first; the PepSeA one can take longer, especially when the import brought monomers the similarity matrix has to be rebuilt for.

Both are best-effort. An alignment that cannot run ends as a **Failed** row with its reason, and the dataset itself is never affected. If both fail, import an alignment from a file.

## Which one should I use?

- **Start with what the import gave you.** Both computed alignments are there for free; open each in the alignment editor and keep the one that reads better for your series.
- **Prefer PepSeA** when the series carries many non-natural monomers, or when center-star stacks residues you consider unrelated into one column. It compares the monomers' structures rather than only their natural analog.
- **Prefer center-star** when you want a frame you can predict and explain, when PepSeA is unavailable, or when the dataset exceeds PepSeA's monomer limit.
- **Import a file** when your team already maintains a curated alignment, or when neither computed frame is right and correcting it by hand would take longer than writing it.

A computed alignment is a **starting point, not a verdict**: whichever you pick, you can correct it in the alignment editor and save it as a new alignment.

## How branches are aligned

Both aligners treat branches the same way. The backbone is aligned first. Each branch's attachment point is then translated into the aligned backbone **column** it hangs off, and the branches attached at the *same* column are aligned together, as a group of their own.

Branches at different columns are never mixed — a branch hanging off position 5 is never compared with one hanging off position 12, because they are not the same feature of the molecule. This is what the *x*/*y* branches-aligned count on an alignment row refers to.

An imported alignment takes its branches from the Excel sheets you map to them instead.

## The life of a computed alignment

A computed alignment is queued, then run by a worker in the background, so its row appears in the list before it is ready:

| Row shows | Meaning |
| --- | --- |
| **In progress** | Queued or running. Click its progress icon to follow the steps. |
| *(no status)* | Completed: the alignment can be selected for a SAR Slide and opened in the editor. |
| **Failed** | It did not run to the end. Click the red icon to read why, then delete the row and run a new one. |
| **Replaced** | A PepSeA request that never started: either a newer request on the same dataset took its place — its arrow icon takes you there — or its parameters were never submitted. |

Only a completed alignment can carry a SAR Slide. When you create a SAR Report, the newest completed alignment is preselected; pick another one in the list if you prefer.

Computing an alignment always **adds** one — it never overwrites an existing alignment, and imported alignments are never touched.

## Where to go next

- [How to Align Peptides](/public/docs/how-to-align-peptides) — creating, importing, reviewing and repairing an alignment
- [Understanding Center-Star Alignment](/public/docs/explanation-understanding-center-star-alignment)
- [Understanding PepSeA Alignment](/public/docs/explanation-understanding-pepsea-alignment)
- [Understanding Peptides in Ideation](/public/docs/explanation-understanding-peptides) — the wider concepts: HELM and monomers, backbone and branches, hotspots, synergies and clustering
- [How to Create a Peptide SAR Report](/public/docs/how-to-create-peptide-sar-report)