hydropathy

README

Module name: assessment-hydropathy

Measures the average hydropathy of proteins in a SAINT file and a BioPlex dataset

parameters	definition	default
bioplexFile	BioPlex dataset
database	sequence database in fasta format
FDR	FDR threshold for significant interactors	0.01
saintFile	SAINT file

Example file formats

bioplexFile

GeneA	GeneB	UniprotA	UniprotB	SymbolA	SymbolB	p(Wrong)	p(No Interaction)	p(Interaction)
100	728378	P00813	A5A3E0	ADA	POTEF	2.38085788908859e-9	0.000331855941652957	0.999668141677489
100	345651	P00813	Q562R1	ADA	ACTBL2	9.78643725788521e-18	0.211914436568748	0.788085563431252
222389	708	Q8N7W2	Q07021	BEND7	C1QBP	2.96221526059856e-17	0.00564451180569955	0.994355488194301
222389	4038	Q8N7W2	O75096	BEND7	LRP4	3.30299445393738e-10	0.000280259555661228	0.999719740114039
645121	3312	Q6ZMN8	P11142	CCNI2	HSPA8	2.06028533960837e-16	0.0362347656743182	0.963765234325682
645121	55132	Q6ZMN8	Q659C4-2	CCNI2	LARP1B	1.54566627347441e-12	0.0315484115050354	0.968451588493419
645121	1020	Q6ZMN8	Q00535	CCNI2	CDK5	7.11903595597094e-10	0.0000638718598341267	0.999936127428262
945	201266	P20138	Q8N1S5	CD33	SLC39A11	3.13297318944057e-11	0.0864322481626163	0.913567751806054

database

>NP_001263222.1|gn|NISCH:11188| nischarin isoform 2 [Homo sapiens]
MATARTFGPEREAEPAKEARVVGSELVDTYTVYIIQVTDGSHEWTVKHRYSDFHDLHEKLVAERKIDKNL
LPPKKIIGKNSRSLVEKREKDLEVYLQKLLAAFPGVTPRVLAHFLHFHFYEINGITAALAEELFEKGEQL
LGAGEVFAIGPLQLYAVTEQLQQGKPTCASGDAKTDLGHILDFTCRLKYLKVSGTEGPFGTSNIQEQLLP
FDLSIFKSLHQVEISHCDAKHIRGLVASKPTLATLSVRFSATSMKEVLVPEASEFDEWEPEGTTLEGPVT
AVIPTWQALTTLDLSHNSISEIDESVKLIPKIEFLDLSHNGLLVVDNLQHLYNLVHLDLSYNKLSSLEGL
HTKLGNIKTLNLAGNLLESLSGLHKLYSLVNLDLRDNRIEQMEEVRSIGSLPCLEHVSLLNNPLSIIPDY
RTKVLAQFGERASEVCLDDTVTTEKELDTVEVLKAIQKAKEVKSKLSNPEKKGGEDSRLSAAPCIRPSSS
PPTVAPASASLPQPILSNQGNRVCILLLVEPHSPAWAPWLGWGWGRGASTCFQQGQTQGGQCLLQAGPRG
GTHGRGAWPDASCCLLGEDSQLL
>NP_001263218.1|gn|PRKAR1A:5573| cAMP-dependent protein kinase type I-alpha regulatory subunit isoform a [Homo sapiens]
MESGSTAASEEARSLRECELYVQKHNIQALLKDSIVQLCTARPERPMAFLREYFERLEKEEAKQIQNLQK
AGTRTDSREDEISPPPPNPVVKGRRRRGAISAEVYTEEDAASYVRKVIPKDYKTMAALAKAIEKNVLFSH
LDDNERSDIFDAMFSVSFIAGETVIQQGDEGDNFYVIDQGETDVYVNNEWATSVGEGGSFGELALIYGTP
RAATVKAKTNVKLWGIDRDSYRRILMGSTLRKRKMYEEFLSKVSILESLDKWERLTVADALEPVQFEDGQ
KIVVQGEPGDEFFIILEGSAAVLQRRSENEEFVEVGRLGPSDYFGEIALLMNRPRAATVVARGPLKCVKL
DRPRFERVLGPCSDILKRNIQQYNSFVSLSV

Output

• stdout

Documentation

Overview

Package hydropathy calculates the average hydropathy of proteins sequences

Index

• func Assess(fileOptions map[string]interface{})

Functions

func Assess

func Assess(fileOptions map[string]interface{})

Assess the hyrdropathy of protein sequences in a SAINT and BioPlex file using the scale of Kyte J. and Doolittle R.F. J. Mol. Biol. 157:105-132(1982).