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

Description Usage Format Source References Examples

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

1

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

1
2

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.