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README.txt 2022-05-12 1.4 kB
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FAQ-Galaxy.pdf 2021-12-09 660.5 kB
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FAQ-Java-GUI.pdf 2021-12-09 509.1 kB
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epibuilder-1.1.jar 2021-12-09 64.2 MB
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epibuilder-gui-1.1.jar 2021-12-09 64.2 MB
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Totals: 5 Items   129.6 MB 0 
#Required Java 8 ou Higher
#Run as GUI (Recommended)
java -jar epibuilder-gui-1.1.jar

#Run as TERMINAL

java -jar epibuilder-1.1.jar -b file-from-bepipred.txt -f your_run_name -p "PARKER:d;CHOU_FOSMAN:d;EMINI:d;KARPLUS_SCHULZ:d;KOLASKAR:d" -t 0.5 -min_len 10 -max_len 30 -proteomes "proteome1=proteome1.fasta;proteome2=proteome2.fasta" -blast "task=blastp-short;identity=90;cover=90;word-size=4;makeblastdb_path=makeblastdb;blastp_path=blastp"
#Parameters

-b: the source of BepiPred-2.0
	#If you are have a csv file from BepiPred-2.0 online, add the option '-o'
-f: name of your run, all files will be generated using this prefix
-p: additional softwares, the d value means default value for the method, it is possible to set a number instead
-t: optional - threshold for the assembly (default 0.6)
-min_len: optional - min epitope length (default 10)
-max_len: optional - max epitope length (default 30)
-proteomes: optional - proteomes for search, use this pattern: "<alias1>=<location1.fasta>;<alias2>=<location2.fasta>"
-blast: optional - if you know what is blast, you will know how to set this 

Please cite us: 

Moreira RS, Filho VB, Calomeno NA, Wagner G, Miletti LC. 
EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes. 
Bioinform Biol Insights. 2022;16:117793222210952. doi:10.1177/11779322221095221

https://doi.org/10.1177/11779322221095221
Source: README.txt, updated 2022-05-12