BioJava:CookBook:AAPROP:commandprompt

From BioJava

How can I compute physico-chemical properties using Command Prompt?

1) Download biojava3-aa-prop-3.0.2-SNAPSHOT-jar-with-dependencies.jar and rename it to AAProperties.jar
2) Study the Manual section below
Note: Test.fasta is available if you would need sample fasta sequences.

Manual

NAME

An executable to generate physico-chemical properties of protein sequences.

EXAMPLES

java -jar AAProperties.jar -i test.fasta -a
	Generates all possible properties.

java -jar AAProperties.jar -i test.fasta -1 -3 -7
	Generates only molecular weight, extinction coefficient and isoelectric point.

java -jar AAProperties.jar -i test.fasta -0 A -0 N -1
	Generates composition of two specific amino acid symbol and molecular weight.

OPTIONS

Required
	-i location of input FASTA file

Optional
	-o location of output file [standard output (default)]
	-f output format [csv (default) or tsv]
	-x location of Amino Acid Composition XML file for defining amino acid composition
	-y location of Element Mass XML file for defining mass of elements
	-d number of decimals (int) [4 (default)]

Provide at least one of them
	-a compute properties of option 1-9
	-1 compute molecular weight
	-2 compute absorbance
	-3 compute extinction coefficient
	-4 compute instability index
	-5 compute apliphatic index
	-6 compute average hydropathy value
	-7 compute isoelectric point
	-8 compute net charge at pH 7
	-9 compute composition of 20 standard amino acid (A, R, N, D, C, E, Q, G, H, I, L, K, M, F, P, S, T, W, Y, V)
	-0 compute composition of specific amino acid symbol