CView: test case dataset

Summary

All North American subtype B gp120 sequences, verified to be CCR5-using sequences (n = 636), were downloaded from the Los Alamos HIV sequence database in aligned fasta format [1]. These were loaded into CView, using the “Load (fasta)” option of the “All Sequences” menu, following which they were saved in unaligned format using the “Save (unaligned)” option of the “All Sequences” menu. Additionally, the titles of these sequences were saved to a separate file using the “Save (titles)” option. This was repeated for CXCR4-using sequences (n = 76). In order to make sites directly comparable between the two sets of unaligned sequences, they were combined into a single file and aligned using MUSCLE [2].

This alignment was used in the test case example of our CView paper [3] titled “CView: A network based tool for enhanced alignment visualization” (view).

The CView project page is located at: https://sourceforge.net/projects/cview/

A poster sumarization presented at ISMB 2022 is available here.

Tutorials

1. A demonstration of CView usage in the form of an mp4 movie is available here.

2. A demonstration of how variants can be identified using CView is available here.

Related software to this project are:
1. CStone 
2. CSReadGen
3. CView <
4. ChimSim
5. TVScript

General details of the project are available here.

References

1. Kuiken C, Korber B, Shafer RW. HIV Sequence Databases. AIDS Rev. 2003;5: 52. Available: /pmc/articles/PMC2613779/

2. Edgar R. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. doi:10.1093/NAR/GKH340

3. Linheiro, R., Sabatino, S., LoboID, D., & ArcherID, J. (2022). CView: A network based tool for enhanced alignment visualization. PLOS ONE, 17(6), e0259726. https://doi.org/10.1371/JOURNAL.PONE.0259726

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