dbPUP download index README.txt (by Bo Zheng, zbbrian@outlook.com, 06/24/2021)
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website URL: http://bcb.unl.edu/dbpup/

This directory contains 1 subdirecotries and 4 files:

##  Experimentally characterized PUPs can be found in: 

- Characterization.tar.gz
	- characterized_sequences.dat : Protein information file (Swissprot format) of experimentally characterized PUPs.
	-characterized_sequences.fasta : Protein sequence FASTA file of experimentally characterized PUPs.

## Sequence homologs curated by characterized PUPs can be found:

- Swiss-Prot.tar.gz
	- [class_name]
		- [family_name]
			- [family_name].fa : Sequence homologs FASTA file of specific family.
			- [family_name].newick : Phylogenetic tree file of sequence homologs in this family, generated by FastTree.

- TrEMBL.tar.gz
	- [class_name]
		- [family_name]
			- [family_name].fa : Sequence homologs FASTA file of specific family.
			
### All-versus-all BLAST results used for sequence similarity network can be found:

- Sequence_Similarity_Network.tar.gz
	- [class_name]
		- [family_name].tbl : All-versus-all BLAST results for visualization in Cytoscape.
	
### Sequence homologs and PCGs curated from UHGP can be found:

- UHGP/
	- UHGP_Homologs.fa : Sequence homologs FASTA file.
	- PGCs.tar.gz
		- PGC_XXX.fa : PGC protein sequences FASTA file