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This function calculates the Dipeptide Composition descriptor (dim: 400).

Usage

extractDC(x)

Arguments

x

A character vector, as the input protein sequence.

Value

A length 400 named vector

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