extrProtDC: Dipeptide Composition Descriptor
In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
View source: R/502-extractProtDC.R
Description
Dipeptide Composition Descriptor
Usage
1
extrProtDC(x)
Arguments
x
A character vector, as the input protein sequence.
Details
This function calculates the Dipeptide Composition descriptor (Dim: 400).
Value
A length 400 named vector
Author(s)
Min-feng Zhu <wind2zhu@163.com>,
Nan Xiao <http://r2s.name>
References
M. Bhasin, G. P. S. Raghava.
Classification of Nuclear Receptors Based on
Amino Acid Composition and Dipeptide Composition.
Journal of Biological Chemistry, 2004, 279, 23262.
See Also
See extrProtTC for tripeptide composition descriptors.
Examples
1
2
x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
extrProtDC(x)
Example output
OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed
AA RA NA DA CA EA
0.003565062 0.003565062 0.000000000 0.007130125 0.003565062 0.003565062
QA GA HA IA LA KA
0.007130125 0.007130125 0.001782531 0.003565062 0.001782531 0.001782531
MA FA PA SA TA WA
0.000000000 0.005347594 0.003565062 0.007130125 0.003565062 0.000000000
YA VA AR RR NR DR
0.000000000 0.000000000 0.003565062 0.007130125 0.005347594 0.001782531
CR ER QR GR HR IR
0.005347594 0.005347594 0.000000000 0.007130125 0.001782531 0.003565062
LR KR MR FR PR SR
0.005347594 0.001782531 0.001782531 0.003565062 0.001782531 0.003565062
TR WR YR VR AN RN
0.003565062 0.000000000 0.005347594 0.003565062 0.001782531 0.003565062
NN DN CN EN QN GN
0.000000000 0.005347594 0.001782531 0.000000000 0.001782531 0.005347594
HN IN LN KN MN FN
0.003565062 0.000000000 0.003565062 0.001782531 0.000000000 0.001782531
PN SN TN WN YN VN
0.000000000 0.001782531 0.003565062 0.003565062 0.000000000 0.000000000
AD RD ND DD CD ED
0.003565062 0.005347594 0.003565062 0.003565062 0.001782531 0.001782531
QD GD HD ID LD KD
0.000000000 0.005347594 0.001782531 0.001782531 0.001782531 0.001782531
MD FD PD SD TD WD
0.001782531 0.001782531 0.007130125 0.005347594 0.001782531 0.000000000
YD VD AC RC NC DC
0.001782531 0.000000000 0.003565062 0.005347594 0.000000000 0.001782531
CC EC QC GC HC IC
0.003565062 0.003565062 0.003565062 0.001782531 0.001782531 0.001782531
LC KC MC FC PC SC
0.007130125 0.001782531 0.000000000 0.001782531 0.000000000 0.007130125
TC WC YC VC AE RE
0.005347594 0.005347594 0.007130125 0.005347594 0.003565062 0.000000000
NE DE CE EE QE GE
0.000000000 0.001782531 0.003565062 0.003565062 0.005347594 0.003565062
HE IE LE KE ME FE
0.001782531 0.000000000 0.000000000 0.003565062 0.000000000 0.001782531
PE SE TE WE YE VE
0.001782531 0.007130125 0.003565062 0.001782531 0.001782531 0.003565062
AQ RQ NQ DQ CQ EQ
0.008912656 0.001782531 0.000000000 0.001782531 0.005347594 0.001782531
QQ GQ HQ IQ LQ KQ
0.003565062 0.001782531 0.001782531 0.000000000 0.003565062 0.000000000
MQ FQ PQ SQ TQ WQ
0.000000000 0.001782531 0.003565062 0.005347594 0.001782531 0.001782531
YQ VQ AG RG NG DG
0.003565062 0.000000000 0.005347594 0.007130125 0.003565062 0.003565062
CG EG QG GG HG IG
0.007130125 0.003565062 0.003565062 0.008912656 0.000000000 0.001782531
LG KG MG FG PG SG
0.010695187 0.001782531 0.000000000 0.001782531 0.005347594 0.012477718
TG WG YG VG AH RH
0.000000000 0.001782531 0.001782531 0.001782531 0.003565062 0.000000000
NH DH CH EH QH GH
0.001782531 0.000000000 0.003565062 0.000000000 0.003565062 0.000000000
HH IH LH KH MH FH
0.001782531 0.001782531 0.001782531 0.005347594 0.000000000 0.000000000
PH SH TH WH YH VH
0.001782531 0.001782531 0.001782531 0.000000000 0.000000000 0.001782531
AI RI NI DI CI EI
0.003565062 0.001782531 0.000000000 0.003565062 0.000000000 0.003565062
QI GI HI II LI KI
0.000000000 0.005347594 0.000000000 0.001782531 0.003565062 0.000000000
MI FI PI SI TI WI
0.003565062 0.000000000 0.000000000 0.000000000 0.000000000 0.003565062
YI VI AL RL NL DL
0.001782531 0.003565062 0.008912656 0.007130125 0.001782531 0.001782531
CL EL QL GL HL IL
0.005347594 0.001782531 0.003565062 0.010695187 0.003565062 0.007130125
LL KL ML FL PL SL
0.007130125 0.000000000 0.001782531 0.001782531 0.001782531 0.001782531
TL WL YL VL AK RK
0.001782531 0.001782531 0.001782531 0.005347594 0.003565062 0.000000000
NK DK CK EK QK GK
0.000000000 0.000000000 0.000000000 0.003565062 0.005347594 0.008912656
HK IK LK KK MK FK
0.001782531 0.001782531 0.005347594 0.000000000 0.001782531 0.001782531
PK SK TK WK YK VK
0.000000000 0.001782531 0.001782531 0.000000000 0.000000000 0.001782531
AM RM NM DM CM EM
0.001782531 0.001782531 0.003565062 0.000000000 0.000000000 0.000000000
QM GM HM IM LM KM
0.001782531 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
MM FM PM SM TM WM
0.000000000 0.000000000 0.000000000 0.001782531 0.000000000 0.000000000
YM VM AF RF NF DF
0.000000000 0.000000000 0.000000000 0.005347594 0.000000000 0.001782531
CF EF QF GF HF IF
0.003565062 0.003565062 0.001782531 0.001782531 0.000000000 0.001782531
LF KF MF FF PF SF
0.001782531 0.001782531 0.000000000 0.000000000 0.001782531 0.000000000
TF WF YF VF AP RP
0.000000000 0.000000000 0.003565062 0.003565062 0.000000000 0.005347594
NP DP CP EP QP GP
0.005347594 0.000000000 0.001782531 0.001782531 0.001782531 0.003565062
HP IP LP KP MP FP
0.001782531 0.000000000 0.005347594 0.005347594 0.000000000 0.001782531
PP SP TP WP YP VP
0.003565062 0.005347594 0.001782531 0.000000000 0.001782531 0.007130125
AS RS NS DS CS ES
0.003565062 0.007130125 0.007130125 0.005347594 0.007130125 0.005347594
QS GS HS IS LS KS
0.001782531 0.001782531 0.003565062 0.005347594 0.005347594 0.003565062
MS FS PS SS TS WS
0.000000000 0.001782531 0.007130125 0.010695187 0.001782531 0.001782531
YS VS AT RT NT DT
0.007130125 0.001782531 0.001782531 0.005347594 0.000000000 0.005347594
CT ET QT GT HT IT
0.003565062 0.000000000 0.000000000 0.005347594 0.000000000 0.000000000
LT KT MT FT PT ST
0.005347594 0.001782531 0.001782531 0.000000000 0.000000000 0.005347594
TT WT YT VT AW RW
0.000000000 0.001782531 0.003565062 0.003565062 0.000000000 0.000000000
NW DW CW EW QW GW
0.001782531 0.003565062 0.003565062 0.000000000 0.000000000 0.000000000
HW IW LW KW MW FW
0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
PW SW TW WW YW VW
0.007130125 0.003565062 0.003565062 0.000000000 0.000000000 0.000000000
AY RY NY DY CY EY
0.001782531 0.000000000 0.005347594 0.000000000 0.005347594 0.003565062
QY GY HY IY LY KY
0.001782531 0.001782531 0.000000000 0.001782531 0.003565062 0.003565062
MY FY PY SY TY WY
0.000000000 0.001782531 0.001782531 0.003565062 0.003565062 0.000000000
YY VY AV RV NV DV
0.000000000 0.003565062 0.001782531 0.003565062 0.000000000 0.003565062
CV EV QV GV HV IV
0.001782531 0.001782531 0.001782531 0.001782531 0.003565062 0.001782531
LV KV MV FV PV SV
0.003565062 0.003565062 0.000000000 0.003565062 0.003565062 0.003565062
TV WV YV VV
0.005347594 0.000000000 0.001782531 0.003565062
BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/502-extractProtDC.R
Description
Dipeptide Composition Descriptor
Usage
1 | extrProtDC(x)
|
Arguments
x |
A character vector, as the input protein sequence. |
Details
This function calculates the Dipeptide Composition descriptor (Dim: 400).
Value
A length 400 named vector
Author(s)
Min-feng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>
References
M. Bhasin, G. P. S. Raghava. Classification of Nuclear Receptors Based on Amino Acid Composition and Dipeptide Composition. Journal of Biological Chemistry, 2004, 279, 23262.
See Also
See extrProtTC for tripeptide composition descriptors.
Examples
1 2 | x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
extrProtDC(x)
|
Example output
OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed
AA RA NA DA CA EA
0.003565062 0.003565062 0.000000000 0.007130125 0.003565062 0.003565062
QA GA HA IA LA KA
0.007130125 0.007130125 0.001782531 0.003565062 0.001782531 0.001782531
MA FA PA SA TA WA
0.000000000 0.005347594 0.003565062 0.007130125 0.003565062 0.000000000
YA VA AR RR NR DR
0.000000000 0.000000000 0.003565062 0.007130125 0.005347594 0.001782531
CR ER QR GR HR IR
0.005347594 0.005347594 0.000000000 0.007130125 0.001782531 0.003565062
LR KR MR FR PR SR
0.005347594 0.001782531 0.001782531 0.003565062 0.001782531 0.003565062
TR WR YR VR AN RN
0.003565062 0.000000000 0.005347594 0.003565062 0.001782531 0.003565062
NN DN CN EN QN GN
0.000000000 0.005347594 0.001782531 0.000000000 0.001782531 0.005347594
HN IN LN KN MN FN
0.003565062 0.000000000 0.003565062 0.001782531 0.000000000 0.001782531
PN SN TN WN YN VN
0.000000000 0.001782531 0.003565062 0.003565062 0.000000000 0.000000000
AD RD ND DD CD ED
0.003565062 0.005347594 0.003565062 0.003565062 0.001782531 0.001782531
QD GD HD ID LD KD
0.000000000 0.005347594 0.001782531 0.001782531 0.001782531 0.001782531
MD FD PD SD TD WD
0.001782531 0.001782531 0.007130125 0.005347594 0.001782531 0.000000000
YD VD AC RC NC DC
0.001782531 0.000000000 0.003565062 0.005347594 0.000000000 0.001782531
CC EC QC GC HC IC
0.003565062 0.003565062 0.003565062 0.001782531 0.001782531 0.001782531
LC KC MC FC PC SC
0.007130125 0.001782531 0.000000000 0.001782531 0.000000000 0.007130125
TC WC YC VC AE RE
0.005347594 0.005347594 0.007130125 0.005347594 0.003565062 0.000000000
NE DE CE EE QE GE
0.000000000 0.001782531 0.003565062 0.003565062 0.005347594 0.003565062
HE IE LE KE ME FE
0.001782531 0.000000000 0.000000000 0.003565062 0.000000000 0.001782531
PE SE TE WE YE VE
0.001782531 0.007130125 0.003565062 0.001782531 0.001782531 0.003565062
AQ RQ NQ DQ CQ EQ
0.008912656 0.001782531 0.000000000 0.001782531 0.005347594 0.001782531
QQ GQ HQ IQ LQ KQ
0.003565062 0.001782531 0.001782531 0.000000000 0.003565062 0.000000000
MQ FQ PQ SQ TQ WQ
0.000000000 0.001782531 0.003565062 0.005347594 0.001782531 0.001782531
YQ VQ AG RG NG DG
0.003565062 0.000000000 0.005347594 0.007130125 0.003565062 0.003565062
CG EG QG GG HG IG
0.007130125 0.003565062 0.003565062 0.008912656 0.000000000 0.001782531
LG KG MG FG PG SG
0.010695187 0.001782531 0.000000000 0.001782531 0.005347594 0.012477718
TG WG YG VG AH RH
0.000000000 0.001782531 0.001782531 0.001782531 0.003565062 0.000000000
NH DH CH EH QH GH
0.001782531 0.000000000 0.003565062 0.000000000 0.003565062 0.000000000
HH IH LH KH MH FH
0.001782531 0.001782531 0.001782531 0.005347594 0.000000000 0.000000000
PH SH TH WH YH VH
0.001782531 0.001782531 0.001782531 0.000000000 0.000000000 0.001782531
AI RI NI DI CI EI
0.003565062 0.001782531 0.000000000 0.003565062 0.000000000 0.003565062
QI GI HI II LI KI
0.000000000 0.005347594 0.000000000 0.001782531 0.003565062 0.000000000
MI FI PI SI TI WI
0.003565062 0.000000000 0.000000000 0.000000000 0.000000000 0.003565062
YI VI AL RL NL DL
0.001782531 0.003565062 0.008912656 0.007130125 0.001782531 0.001782531
CL EL QL GL HL IL
0.005347594 0.001782531 0.003565062 0.010695187 0.003565062 0.007130125
LL KL ML FL PL SL
0.007130125 0.000000000 0.001782531 0.001782531 0.001782531 0.001782531
TL WL YL VL AK RK
0.001782531 0.001782531 0.001782531 0.005347594 0.003565062 0.000000000
NK DK CK EK QK GK
0.000000000 0.000000000 0.000000000 0.003565062 0.005347594 0.008912656
HK IK LK KK MK FK
0.001782531 0.001782531 0.005347594 0.000000000 0.001782531 0.001782531
PK SK TK WK YK VK
0.000000000 0.001782531 0.001782531 0.000000000 0.000000000 0.001782531
AM RM NM DM CM EM
0.001782531 0.001782531 0.003565062 0.000000000 0.000000000 0.000000000
QM GM HM IM LM KM
0.001782531 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
MM FM PM SM TM WM
0.000000000 0.000000000 0.000000000 0.001782531 0.000000000 0.000000000
YM VM AF RF NF DF
0.000000000 0.000000000 0.000000000 0.005347594 0.000000000 0.001782531
CF EF QF GF HF IF
0.003565062 0.003565062 0.001782531 0.001782531 0.000000000 0.001782531
LF KF MF FF PF SF
0.001782531 0.001782531 0.000000000 0.000000000 0.001782531 0.000000000
TF WF YF VF AP RP
0.000000000 0.000000000 0.003565062 0.003565062 0.000000000 0.005347594
NP DP CP EP QP GP
0.005347594 0.000000000 0.001782531 0.001782531 0.001782531 0.003565062
HP IP LP KP MP FP
0.001782531 0.000000000 0.005347594 0.005347594 0.000000000 0.001782531
PP SP TP WP YP VP
0.003565062 0.005347594 0.001782531 0.000000000 0.001782531 0.007130125
AS RS NS DS CS ES
0.003565062 0.007130125 0.007130125 0.005347594 0.007130125 0.005347594
QS GS HS IS LS KS
0.001782531 0.001782531 0.003565062 0.005347594 0.005347594 0.003565062
MS FS PS SS TS WS
0.000000000 0.001782531 0.007130125 0.010695187 0.001782531 0.001782531
YS VS AT RT NT DT
0.007130125 0.001782531 0.001782531 0.005347594 0.000000000 0.005347594
CT ET QT GT HT IT
0.003565062 0.000000000 0.000000000 0.005347594 0.000000000 0.000000000
LT KT MT FT PT ST
0.005347594 0.001782531 0.001782531 0.000000000 0.000000000 0.005347594
TT WT YT VT AW RW
0.000000000 0.001782531 0.003565062 0.003565062 0.000000000 0.000000000
NW DW CW EW QW GW
0.001782531 0.003565062 0.003565062 0.000000000 0.000000000 0.000000000
HW IW LW KW MW FW
0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000
PW SW TW WW YW VW
0.007130125 0.003565062 0.003565062 0.000000000 0.000000000 0.000000000
AY RY NY DY CY EY
0.001782531 0.000000000 0.005347594 0.000000000 0.005347594 0.003565062
QY GY HY IY LY KY
0.001782531 0.001782531 0.000000000 0.001782531 0.003565062 0.003565062
MY FY PY SY TY WY
0.000000000 0.001782531 0.001782531 0.003565062 0.003565062 0.000000000
YY VY AV RV NV DV
0.000000000 0.003565062 0.001782531 0.003565062 0.000000000 0.003565062
CV EV QV GV HV IV
0.001782531 0.001782531 0.001782531 0.001782531 0.003565062 0.001782531
LV KV MV FV PV SV
0.003565062 0.003565062 0.000000000 0.003565062 0.003565062 0.003565062
TV WV YV VV
0.005347594 0.000000000 0.001782531 0.003565062
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