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Sequence similarity network (SSN) using EFI-EST

KP Ketan D. Patel
AG Andrew M. Gulick
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An initial attempt to generate SSN using BLAST mode of EFI-EST did not include any sequences from eukaryotic phyla and a decrease in stringency led to the inclusion of other types of NRPS-like proteins. Hence, various homologous sequences of CHPAs were collected using BLAST and HMMER search in all bacterial and eukaryotic phyla individually and confirming the presence of NRPS-terminal domain. A list of all combined sequences was uploaded in FASTA mode in EFI-EST (https://efi.igb.illinois.edu/efi-est/#)45,46. All-by-all BLAST was performed by EFI-EST to obtain the similarities between sequence pairs and edge value calculation for SSN. The network file was generated with a sequence length cutoff 1100 to 1800 and an alignment score threshold of 525. Cytoscape was used to view, analyze, and generate images for network analysis.

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