Profile scoring matrix derived from the LOGICOIL training set.

Description

This data set contains the Position Specific Scoring Matrix (PSSM) used as the LOGICOIL training set. This dataset was compiled from the CC+ coiled-coil database. This PSSM is used by LOGICOIL to predict the oligomeric state of coiled-coil sequences. More details on the training set can be found in the reference below.

Usage

data(pssm)

Format

A data frame with 20295 observations on the following 18 variables.

amino

a factor with levels A C D E F G H I K L M N P Q R S T V W X Y

register

a factor with levels a b c d e f g

ab

a factor with levels 0 AE IR NL

bc

a factor with levels 0 ES

cd

a factor with levels 0 LT QN

de

a factor with levels 0 EL HD ID IK IL KD LK LQ NT SE TD TN TT

ef

a factor with levels 0 FG IT QG TT YK

fg

a factor with levels 0 KE KN LM QI RH RS SK TN TV

ga

a factor with levels 0 EN KV NK RV VA VI YL

ad

a factor with levels 0 AF AT IL LI LK LS NL RL VL

be

a factor with levels 0 AE KE QN RQ

cf

a factor with levels 0 SA

dg

a factor with levels 0 EH LE

ea

a factor with levels 0 IV YA

ae

a factor with levels 0 KI KQ LE LT NR YF

bf

a factor with levels 0 AK ED IH VT

cg

a factor with levels 0 DR EH EI HE MA QE VT

da

a factor with levels 0 II IL IS KI LK LN LR LV NI VI YA YT

Source

DOI: 10.1093/bioinformatics/bts648

References

Thomas L. Vincent, Peter J. Green and Dek N. Woolfson. "LOGICOIL-multi-state prediction of coiled-coil oligomeric state", 29(1), pp69-76, Bioinformatics, (2013).

Examples

data(pssm)
head(pssm, 10)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(LOGICOIL)
Loading required package: nnet
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LOGICOIL/pssm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pssm
> ### Title: Profile scoring matrix derived from the LOGICOIL training set.
> ### Aliases: pssm
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(pssm)
> head(pssm, 10)
   amino register ab bc cd de ef fg ga ad be cf dg ea ae bf cg da
1      M        a  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
2      M        b  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
3      N        c  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
4      L        d  0  0  0 LQ  0  0  0  0  0  0  0  0  0  0  0  0
5      Q        e  0  0  0 LQ  0  0  0  0  0  0  0  0  0  0  0  0
6      T        f  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
7      K        g  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
8      I        a  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
9      D        b  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
10     A        c  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>