This function calculates the Dipeptide Composition descriptor (dim: 400).
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 extractAAC and extractTC
for Amino Acid Composition and Tripeptide Composition descriptors.
Author
Nan Xiao <https://nanx.me>
Examples
x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
extractDC(x)
#> 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