Ali2D

BioCodeKb - Bioinformatics Knowledgebase

Ali2D is a web-server for visualizing and comparing secondary structure predictions. It provides two main functionalities: 2D-alignment and compare predictions. The “2D-alignment” has been designed to visualize conserved secondary structure elements in a multiple sequence alignment (MSA). From this we can study the secondary structure content of homologous proteins (a protein family) and highlight its structural patterns. The “compare predictions” has been designed to compare the output of several secondary structure prediction tools, and check their accuracy when compared with real secondary structure elements extracted from 3D-structure.


Recently, MPI bioinformatics Toolkit proposed two tools: Ali2D and Quick2D. Ali2D allows users to visualize SS conservation in a MSA, where SSE predictions of each sequence in the MSA are produced by PSIPRED, and Quick2D compares the SSE predictions of four tools:

  • PSIPRED

  • SPIDER2

  • PSSPred

  • DeepCNF-SS


Although Ali2D and Quick2D have become important resources for SS prediction, their visualization system is very simple and both are limited to a fixed number of prediction tools. Ali2D adopts the standard format for SSEs based on the three-state codes: H for α-helix, E β-sheets, and C for coil regions. Since these three-state codes can be derived from the output of SS tools, Ali2D works for any tool. Moreover, Ali2D does not run prediction tools, but import their outputs, being extremely fast and providing an easy and interpretable picture that can be downloaded in many formats. Ali2D outputs are used by the 2dSS for producing a more user-friendly graphical representation for SSEs.


The web-server has two main functionalities: “view 2D-alignment” that addresses the item that is, it allows users to visualize and compare SSEs in a set of aligned sequences (a protein family) and “compare predictions” that compares SS predictions of many tools and allowing to check the prediction accuracy. In any case, users can set colors for SSEs and save their pictures in SVG format, for a posterior edition, or in other image format such as PNG, and PDF.


Given a MSA, representing a protein family, and the predicted SSEs of its constituent sequences, we can map each SSE onto a MSA position to obtain a 2D-alignment. In it, the user provides a MSA in Fasta or Clustalw format and the SSE predictions of each aligned sequence, to obtain a 2D-alignment that shows the SS conservation for that MSA. The 2D-alignment highlights the secondary structure conservation in a set of related sequences, where is possible to see how SSEs of homologous proteins are aligned. In particular, it can be used to compare structurally homologous proteins with low sequence identity and detect their SS patterns. Proteins with even  less than 30% of sequence identity, can still observe SSE conservation among different protein sequences.


In the Ali2D website, we can insert our unaligned sequences and the tool will align them and predict their 2D structures. Blue indicates beta strands while red indicates alpha helices. Color saturation is proportional to prediction confidence.


To obtain Ali2D output, click on the tab "Text Output" and save all information in a local file. Next, the local file can be uploaded on the website.

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