Ejercicio1
Alessandro Giuffra, Alessandra Meza, Diana Peña, Luis Quesada
12/9/2020
#Inicialización de variables y carga de librerías
Carga de paquetes
library(seqinr)## Warning: package 'seqinr' was built under R version 3.5.3library(ape)##
## Attaching package: 'ape'## The following objects are masked from 'package:seqinr':
##
## as.alignment, consensusSelección de secuencia
El desarrollo de las gráficas de caracerísticas de una secuencia serán realizadas de la proteina: Multifunctional 2-oxoglutarate metabolism enzyme.
path <- "D:/OCTAVO CICLO/Bioinformatica/CLASE 2/data/A0PVU7.fasta.txt"
oxa <- seqinr::read.fasta(path,seqtype="AA")Tabla de contingencia de valores
##
## A C D E F G H I K L M N P Q R S T V W Y
## 122 8 75 84 48 95 32 63 56 106 27 45 76 51 82 68 60 93 13 34Frecuencia absoluta
A continuación se muestran las gráficas de la frecuencia absoluta de los datos de la proteína utilizada.
##
## C W M H Y N F Q K T I S D P R E V G L A
## 8 13 27 32 34 45 48 51 56 60 63 68 75 76 82 84 93 95 106 122
Frecuencia relativa
A continuación se muestra la gráfica de la frecuencia relativa de la secuencia.
Utilizando SEQINR
Se utilizó el banco Swissprot para importar la proteína y sus palabras claves que son Acyltransferasa y Mycobacterium ulcerans en humanos.
# Importar desde base de datos remota
library(seqinr)
seqinr::choosebank("swissprot") # Se utiliza el banco de swissprot
app2 <- query("app2","K=Acyltransferase AND sp=Mycobacterium ulcerans") # Nombre de la proteína
summary(app2) #Resumen de los datos## Length Class Mode
## call 3 -none- call
## name 1 -none- character
## nelem 1 -none- numeric
## typelist 1 -none- character
## req 10 -none- list
## socket 1 sockconn numericUtilizando APE
Se utilizó la librería APE para importar listas múltiples de genes relacionados al Myc Ulcerans en humanos
#Importando listas múltiples usando APE
acs.num <- c("AF177765.1","AF177766.1 ","AH009665.2","AL160272.16","CH471090.1")
library(ape)
myco <- ape::read.GenBank(acs.num, as.character = T) Analizando los datos que se obtuvieron con APE:
summary(myco) #Resumen de datos## Length Class Mode
## AF177765.1 18974 -none- character
## AF177766.1 2576 -none- character
## AH009665.2 9679 -none- character
## AL160272.16 146978 -none- character
## CH471090.1 25070985 -none- characternames(myco)# Nombres de las secuencias## [1] "AF177765.1" "AF177766.1 " "AH009665.2" "AL160272.16" "CH471090.1"round(table(myco$AF177765.1)/length(myco$AF177765.1)*100,1)##
## a c g t
## 30.4 19.0 19.3 31.3Generar PDF con tablas de valores de las 5 secuencias.
##
## a c g t
## 30.4 19.0 19.3 31.3##
## a c g t
## 5760 3607 3669 5938##
## a c g t
## 735 535 537 769##
## a c g n t
## 2808 1840 1870 212 2949##
## a c g t
## 43340 28974 29081 45583##
## a c g n t
## 6602494 5832829 5846425 194611 6594626## png
## 2Análisis estadístico
Análisis RHO
Frecuencia relativa de los aminoácidos, muestra los nucleótidos más representativos. Se utilizó Z score para que se vea más clara la escala de los datos mostrados.
##
## aaa aac aag aat aca acc acg act
## 1.2171067 0.9025967 1.2334085 0.9229322 1.1372718 0.9849239 0.1511462 0.9893602
## aga agc agg agt ata atc atg att
## 1.3398898 1.1099799 1.4209117 0.9066513 0.7803803 0.7821491 1.1878279 0.9183124
## caa cac cag cat cca ccc ccg cct
## 1.0710814 1.1290591 1.6720548 1.1206912 1.4317430 1.3119620 0.1961087 1.4400898
## cga cgc cgg cgt cta ctc ctg ctt
## 0.1369762 0.1131397 0.2002100 0.2015961 0.8025784 1.3375591 1.5715335 1.2852656
## gaa gac gag gat gca gcc gcg gct
## 1.3014383 0.8596440 1.3048241 0.7631938 1.1572130 1.1464818 0.2150404 1.1591778
## gga ggc ggg ggt gta gtc gtg gtt
## 1.3233982 1.2605815 1.3486280 0.9098700 0.7029416 0.8338749 1.2296757 0.7737137
## taa tac tag tat tca tcc tcg tct
## 0.7785527 0.6916766 0.7402406 0.8367634 1.1907344 1.2862938 0.1282884 1.2965896
## tga tgc tgg tgt tta ttc ttg ttt
## 1.1562673 1.1866682 1.4593954 1.1577874 0.7906705 1.2229840 1.0353291 1.2433153
##
## aa ac ag at ca cc cg
## 4.111186 -4.260692 5.878549 -4.136356 7.071825 5.587602 -22.055523
## ct ga gc gg gt ta tc
## 6.850786 1.683642 -0.699931 6.177692 -5.023685 -9.647782 1.225455
## tg tt
## 7.489024 3.882597
Análisis: Descubriendo CG(cpG island)
En las gráficas se muestra el porcentaje de GC en diferentes rangos de valores de la lista de genes múltiples importados remotamente con la librería APE.
Estadística de la proteína
## $Compo
##
## * A C D E F G H I K L M N P Q R S T V W
## 0 122 8 75 84 48 95 32 63 56 106 27 45 76 51 82 68 60 93 13
## Y
## 34
##
## $Prop
## $Prop$Tiny
## [1] 0.2851373
##
## $Prop$Small
## [1] 0.5185784
##
## $Prop$Aliphatic
## [1] 0.2116317
##
## $Prop$Aromatic
## [1] 0.1025848
##
## $Prop$Non.polar
## [1] 0.5533118
##
## $Prop$Polar
## [1] 0.4466882
##
## $Prop$Charged
## [1] 0.2657512
##
## $Prop$Basic
## [1] 0.1373183
##
## $Prop$Acidic
## [1] 0.128433
##
##
## $Pi
## [1] 5.911408Tablas de Hidrofobicidad
Se observa la relación entre los aminoácidos de las secuencias y los valores de hidrofobicidad en diferentes escalas.
## Name Three.Letter.Code One.Letter.Code
## 1 Alanine Ala A
## 2 Arginine Arg R
## 3 Asparagine Asn N
## 4 Aspartic Acid Asp D
## 5 Cysteine Cys C
## 6 Glutamic Acid Glu E## Residue.Type kdHydrophobicitya wwHydrophobicityb hhHydrophobicityc
## 1 Ile 4.5 0.31 -0.60
## 2 Val 4.2 -0.07 -0.31
## 3 Leu 3.8 0.56 -0.55
## 4 Phe 2.8 1.13 -0.32
## 5 Cys 2.5 0.24 -0.13
## 6 Met 1.9 0.23 -0.10
## mfHydrophobicityd ttHydrophobicitye
## 1 -1.56 1.97
## 2 -0.78 1.46
## 3 -1.81 1.82
## 4 -2.20 1.98
## 5 0.49 -0.30
## 6 -0.76 1.40## [1] 1.8 -4.5 -3.5 -3.5## three.L Name One.Letter.Code kdHydrophobicitya wwHydrophobicityb
## 1 Ala Alanine A 1.8 -0.17
## 2 Arg Arginine R -4.5 -0.81
## 3 Asn Asparagine N -3.5 -0.42
## 4 Asp Aspartic Acid D -3.5 -1.23
## 5 Cys Cysteine C 2.5 0.24
## 6 Gln Glutamine Q -3.5 -0.58
## hhHydrophobicityc mfHydrophobicityd ttHydrophobicitye Hydro
## 1 0.11 0.00 0.38 0.424
## 2 2.58 3.71 -2.57 -0.318
## 3 2.05 3.47 -1.62 -0.004
## 4 3.49 2.95 -3.27 -0.312
## 5 -0.13 0.49 -0.30 0.560
## 6 2.36 3.01 -1.84 -0.110## [1] "M" "A" "N" "I" "S" "S" "P" "F" "G" "Q" "N" "E" "W" "L" "V" "E" "E" "M"
## [19] "Y" "R" "K" "F" "R" "D" "D" "P" "S" "S" "V" "D" "P" "S" "W" "H" "E" "F"
## [37] "L" "V" "D" "Y" "N" "P" "E" "S" "T" "Q" "E" "A" "T" "E" "P" "A" "V" "V"
## [55] "K" "P" "A" "A" "A" "P" "A" "K" "P" "A" "P" "A" "P" "A" "P" "A" "K" "P"
## [73] "A" "A" "G" "P" "P" "A" "A" "G" "N" "G" "S" "P" "A" "A" "A" "P" "S" "A"
## [91] "K" "P" "A" "A" "A" "P" "A" "K" "A" "P" "A" "P" "P" "P" "A" "E" "G" "D"
## [109] "E" "M" "Q" "V" "L" "R" "G" "A" "A" "A" "A" "V" "V" "K" "N" "M" "S" "A"
## [127] "S" "L" "D" "V" "P" "T" "A" "T" "S" "V" "R" "A" "V" "P" "A" "K" "L" "L"
## [145] "I" "D" "N" "R" "I" "V" "I" "N" "N" "Q" "L" "K" "R" "N" "R" "G" "G" "K"
## [163] "I" "S" "F" "T" "H" "L" "L" "G" "Y" "A" "L" "V" "Q" "A" "V" "K" "K" "F"
## [181] "P" "N" "M" "N" "R" "H" "Y" "L" "D" "V" "D" "G" "K" "P" "N" "A" "V" "T"
## [199] "P" "A" "H" "T" "N" "L" "G" "L" "A" "I" "D" "L" "Q" "G" "K" "D" "G" "K"
## [217] "R" "A" "L" "V" "V" "A" "G" "I" "K" "R" "C" "E" "T" "M" "R" "F" "A" "Q"
## [235] "F" "V" "T" "A" "Y" "E" "D" "I" "V" "R" "R" "A" "R" "D" "G" "K" "L" "T"
## [253] "A" "E" "D" "F" "S" "G" "V" "T" "I" "S" "L" "T" "N" "P" "G" "T" "I" "G"
## [271] "T" "V" "H" "S" "V" "P" "R" "L" "M" "A" "G" "Q" "G" "A" "I" "I" "G" "V"
## [289] "G" "A" "M" "E" "Y" "P" "A" "E" "F" "Q" "G" "A" "S" "E" "E" "R" "I" "A"
## [307] "E" "L" "G" "I" "G" "K" "L" "I" "T" "L" "T" "S" "T" "Y" "D" "H" "R" "I"
## [325] "I" "Q" "G" "A" "E" "S" "G" "D" "F" "L" "R" "T" "I" "H" "Q" "M" "L" "L"
## [343] "A" "D" "E" "F" "W" "D" "E" "I" "F" "R" "E" "L" "S" "I" "P" "Y" "L" "P"
## [361] "V" "R" "W" "R" "P" "D" "N" "P" "D" "S" "I" "V" "D" "K" "N" "A" "R" "I"
## [379] "I" "E" "L" "I" "A" "A" "Y" "R" "N" "R" "G" "H" "L" "M" "A" "D" "I" "D"
## [397] "P" "L" "R" "L" "D" "K" "T" "R" "F" "R" "S" "H" "P" "D" "L" "D" "V" "C"
## [415] "T" "H" "G" "L" "T" "L" "W" "D" "L" "D" "R" "S" "F" "K" "V" "G" "G" "C"
## [433] "F" "A" "G" "P" "Q" "N" "M" "K" "L" "R" "D" "V" "L" "S" "I" "L" "R" "D"
## [451] "T" "Y" "C" "R" "H" "V" "G" "V" "E" "Y" "T" "H" "I" "L" "E" "P" "E" "Q"
## [469] "Q" "Q" "W" "L" "Q" "Q" "R" "V" "E" "A" "K" "H" "V" "K" "P" "T" "V" "A"
## [487] "Q" "Q" "K" "Y" "V" "L" "S" "K" "L" "N" "A" "A" "E" "A" "F" "E" "T" "F"
## [505] "L" "Q" "T" "K" "Y" "V" "G" "Q" "K" "R" "F" "S" "L" "E" "G" "A" "E" "S"
## [523] "V" "I" "P" "M" "M" "D" "A" "A" "I" "D" "Q" "C" "A" "E" "Y" "G" "L" "D"
## [541] "E" "V" "V" "I" "G" "M" "P" "H" "R" "G" "R" "L" "N" "V" "L" "A" "N" "I"
## [559] "V" "G" "K" "P" "Y" "S" "Q" "I" "F" "S" "E" "F" "E" "G" "N" "L" "N" "P"
## [577] "S" "Q" "A" "H" "G" "S" "G" "D" "V" "K" "Y" "H" "L" "G" "A" "T" "G" "V"
## [595] "Y" "L" "Q" "M" "F" "G" "D" "N" "D" "I" "Q" "V" "S" "L" "T" "A" "N" "P"
## [613] "S" "H" "L" "E" "A" "V" "D" "P" "V" "L" "E" "G" "L" "V" "R" "A" "K" "Q"
## [631] "D" "L" "L" "E" "H" "G" "E" "T" "D" "T" "E" "N" "Q" "R" "A" "F" "S" "V"
## [649] "V" "P" "M" "M" "L" "H" "G" "D" "A" "A" "F" "A" "G" "Q" "G" "V" "V" "A"
## [667] "E" "T" "L" "N" "L" "A" "N" "L" "P" "G" "Y" "R" "V" "G" "G" "T" "I" "H"
## [685] "I" "I" "V" "N" "N" "Q" "I" "G" "F" "T" "T" "A" "P" "E" "Y" "S" "R" "S"
## [703] "T" "E" "Y" "C" "T" "D" "V" "A" "K" "T" "I" "G" "A" "P" "I" "F" "H" "V"
## [721] "N" "G" "D" "D" "P" "E" "A" "C" "V" "W" "V" "A" "R" "L" "A" "V" "D" "F"
## [739] "R" "Q" "R" "F" "N" "K" "D" "V" "I" "I" "D" "M" "L" "C" "Y" "R" "R" "R"
## [757] "G" "H" "N" "E" "G" "D" "D" "P" "S" "M" "T" "N" "P" "R" "M" "Y" "D" "V"
## [775] "V" "D" "T" "K" "R" "G" "V" "R" "K" "S" "Y" "T" "E" "A" "L" "I" "G" "R"
## [793] "G" "D" "I" "S" "I" "K" "E" "A" "E" "D" "A" "L" "R" "D" "Y" "Q" "G" "Q"
## [811] "L" "E" "Q" "V" "F" "N" "E" "V" "R" "E" "L" "E" "K" "H" "G" "A" "Q" "P"
## [829] "S" "E" "S" "V" "E" "S" "D" "Q" "M" "I" "P" "A" "G" "L" "A" "T" "A" "V"
## [847] "D" "K" "S" "L" "L" "A" "R" "I" "G" "D" "A" "F" "L" "A" "V" "P" "D" "G"
## [865] "F" "T" "T" "H" "P" "R" "V" "Q" "P" "V" "L" "E" "K" "R" "R" "E" "M" "A"
## [883] "Y" "E" "G" "K" "I" "D" "W" "A" "F" "A" "E" "L" "L" "A" "L" "G" "S" "L"
## [901] "V" "A" "E" "G" "K" "L" "V" "R" "F" "S" "G" "Q" "D" "T" "R" "R" "G" "T"
## [919] "F" "S" "Q" "R" "H" "S" "V" "I" "I" "D" "R" "H" "T" "R" "E" "E" "F" "T"
## [937] "P" "L" "Q" "L" "L" "T" "T" "N" "K" "D" "G" "S" "P" "T" "G" "G" "K" "F"
## [955] "L" "V" "Y" "D" "S" "P" "L" "S" "E" "Y" "A" "A" "V" "G" "F" "E" "Y" "G"
## [973] "Y" "T" "V" "G" "N" "P" "D" "A" "V" "V" "L" "W" "E" "A" "Q" "F" "G" "D"
## [991] "F" "V" "N" "G" "A" "Q" "S" "I" "I" "D" "E" "F" "I" "S" "S" "G" "E" "A"
## [1009] "K" "W" "G" "Q" "L" "S" "N" "V" "V" "L" "L" "L" "P" "H" "G" "H" "E" "G"
## [1027] "Q" "G" "P" "D" "H" "T" "S" "G" "R" "I" "E" "R" "F" "L" "Q" "L" "W" "A"
## [1045] "E" "G" "S" "M" "T" "I" "A" "M" "P" "S" "T" "P" "S" "N" "Y" "F" "H" "L"
## [1063] "L" "R" "R" "H" "A" "L" "D" "G" "I" "Q" "R" "P" "L" "I" "V" "F" "T" "P"
## [1081] "K" "S" "M" "L" "R" "N" "K" "A" "A" "V" "S" "D" "I" "K" "D" "F" "T" "E"
## [1099] "I" "K" "F" "R" "S" "V" "L" "E" "E" "P" "T" "Y" "E" "D" "G" "V" "G" "D"
## [1117] "R" "N" "L" "V" "N" "R" "I" "L" "L" "T" "S" "G" "K" "I" "Y" "Y" "E" "M"
## [1135] "V" "A" "R" "K" "A" "K" "D" "K" "R" "E" "D" "V" "A" "I" "V" "R" "V" "E"
## [1153] "Q" "L" "A" "P" "L" "P" "R" "R" "R" "L" "R" "E" "T" "L" "D" "R" "Y" "P"
## [1171] "N" "A" "K" "E" "F" "F" "W" "V" "Q" "E" "E" "P" "A" "N" "Q" "G" "A" "W"
## [1189] "P" "R" "F" "G" "L" "E" "L" "P" "E" "L" "L" "P" "E" "K" "L" "S" "G" "V"
## [1207] "K" "R" "I" "S" "R" "R" "A" "M" "S" "A" "P" "S" "S" "G" "S" "S" "K" "V"
## [1225] "H" "A" "V" "E" "Q" "Q" "E" "I" "L" "D" "T" "A" "F" "G"Hidropatía de la secuencia
Se observan señales con distintos picos a lo largo del tamaño de la secuencia que relacionan hidropatía vs su posición a diferentes escalas.
Visualización de genes y transcriptos
A través de librerías como Bioconductor, BiocManager y GenomeGraphs podemos visualizar data genomica, a través de regiones pintadas del cromosoma 6 que hacen referencia a proteínas codificantes y no en las mismas zonas de la secuencia de ADN, en este caso usamos la data de homo sapiens y AGPAT4 1-acylglycerol-3-phosphate O-acyltransferase 4 (ENSG00000026652).
## Loading required package: biomaRt##
## Attaching package: 'biomaRt'## The following object is masked from 'package:seqinr':
##
## getSequence## Loading required package: grid
