pssm: Profile scoring matrix derived from the original SCORER 2.0...

In SCORER2: SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences

Description

This data set includes the Profile scoring matrix derived from the training set compiled from the CC+ coiled-coil database. It is used as the default PSSM used by SCORER 2.0 when predicting 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 multi-dimensional array with 7 element, each of dimension 2x21.

Source

DOI: 10.1093/bioinformatics/btr299.

References

Craig T. Armstrong, Thomas L. Vincent, Peter J. Green and Dek N. Woolfson. (2011) SCORER 2.0: an algortihm for distinguishing parallel dimeric and trimeric coiled-coil sequences. Bioinformatics. DOI: 10.1093/bioinformatics/btr299

Examples

	data(pssm)
	print(pssm)

Example output

, , a

        A C D  E  F G H  I  K   L  M  N P  Q  R  S  T  V W  Y X
DIMER  31 9 4 16 18 1 8 74 29 136 14 50 1 10 21 11 18 79 0 12 1
TRIMER  5 0 0  2  5 1 1 40  0  44  5  3 1  4  2  2  3 28 1  2 1

, , b

        A C  D  E  F G H  I  K  L M  N P  Q  R  S  T  V W  Y X
DIMER  56 5 42 75 10 9 6 11 52 18 7 20 3 40 35 32 24 17 1 15 0
TRIMER 21 1 14 16  0 4 1  1 10  7 0  7 0 14 12 14  4  5 0  3 0

, , c

        A C  D  E  F  G  H  I  K  L  M  N P  Q  R  S  T  V W  Y X
DIMER  33 2 29 78 10 12 15 14 44 27 10 19 3 54 40 25 27 20 2 12 2
TRIMER 21 0 15 18  2  2  4  1 10  7  0  9 0 13  6  9  9  6 0  2 0

, , d

        A  C D  E  F G H  I  K   L  M N P  Q  R  S  T  V W  Y X
DIMER  38 10 2 13 10 0 3 20 20 277 21 6 0 11 16 21 17 19 7 14 5
TRIMER 10  0 0  2  2 0 3 25  1  67  5 9 0  6  2  3  3  9 0  1 1

, , e

        A C  D  E  F G H  I  K  L M  N P  Q  R  S  T  V W Y X
DIMER  31 1 20 90 12 3 6 16 59 42 9 10 0 50 38 18 26 13 4 8 5
TRIMER  5 0  9 33  0 3 1  2 14  7 3 11 1 14 11 11  5  5 1 1 0

, , f

        A C  D  E F  G  H I  K  L M  N P  Q  R  S  T  V W Y X
DIMER  48 3 41 77 4 18 11 7 52 29 6 29 1 29 36 26 23 15 1 5 0
TRIMER 11 0 11 19 0  6  1 1 17  5 0  6 0 14  7 20 11  3 1 1 0

, , g

        A C  D   E F G H  I  K  L  M  N P  Q  R  S  T  V W  Y X
DIMER  27 3 12 107 4 3 5 15 64 47 10  7 0 53 38 17 16 19 1 11 1
TRIMER 10 1 12  14 0 3 3  5 21  5  2 11 0  9 18 10  5  3 0  3 0

SCORER2 documentation built on May 2, 2019, 4:06 a.m.