pssm: Profile scoring matrix derived from the LOGICOIL training...

In LOGICOIL: LOGICOIL: multi-state prediction of coiled-coil oligomeric state.

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)

LOGICOIL documentation built on May 2, 2019, 9:09 a.m.