• What is an ORF? What is a CDS?
• How can we read a GFF file on R?
• How can we combine a FASTA file and a GFF file to get the gene sequences?
• What is a Transcription Factor (TF)?
• What is a Binding Site (BS)?
• What is a Motif? What is a Regular Expression?
• What is a Position Specific Score Matrix?
• How do we find Transcription Factor Binding Sites?

• Reading Frame: 6 ways of translate DNA to AA
• Open Reading Frame: Start-Not Stop{repeated}-Stop
• CDS: ORF that is translated

\[\{x\text{ is CDS}\}\subset\{x\text{ is ORF}\}\]

• What are the inputs?

• What is the output?

• What are the steps between them?

• Which ones are CDS?

gff <- read.delim("NC_000913.gff", header=F, comment.char="#")
summary(gff)

           V1            V2                   V3             V4         
 NC_000913.3:9720   RefSeq:9720   gene         :4516   Min.   :      1  
                                  CDS          :4382   1st Qu.:1162247  
                                  repeat_region: 355   Median :2298492  
                                  exon         : 178   Mean   :2313290  
                                  tRNA         :  89   3rd Qu.:3453929  
                                  ncRNA        :  65   Max.   :4640942  
                                  (Other)      : 135                    
       V5          V6       V7       V8      
 Min.   :    255   .:9720   -:4682   .:5338  
 1st Qu.:1163115            +:5038   0:4370  
 Median :2299578                     1:   7  
 Mean   :2314649                     2:   5  
 3rd Qu.:3455647                             
 Max.   :4641652                             
                                             
                                                                                                                                                                                                                                                                          V9      
 ID=cds1219;Parent=gene1262;Note=pseudogene%2C transposase homolog;Dbxref=ASAP:ABE-0004159,ASAP:ABE-0004161,ASAP:ABE-0285106,UniProtKB%2FSwiss-Prot:P30192,EcoGene:EG11611,GeneID:4056037;gbkey=CDS;gene=insZ;pseudo=true;transl_table=11                                  :   3  
 ID=cds1389;Parent=gene1435;Note=pseudogene%2C autotransporter homolog%7Einterrupted by IS2 and IS30;Dbxref=ASAP:ABE-0004680,ASAP:ABE-0004694,ASAP:ABE-0285093,UniProtKB%2FSwiss-Prot:P33666,EcoGene:EG11307,GeneID:2847750;gbkey=CDS;gene=ydbA;pseudo=true;transl_table=11:   3  
 ID=cds1922;Parent=gene1981;Note=pseudogene%2C IpaH%2FYopM family;Dbxref=ASAP:ABE-0006435,ASAP:ABE-0006437,ASAP:ABE-0006440,ASAP:ABE-0285096,UniProtKB%2FSwiss-Prot:P76321,EcoGene:EG13281,GeneID:2847704;gbkey=CDS;gene=yedN;pseudo=true;transl_table=11                  :   3  
 ID=cds3953;Parent=gene4120;Note=pseudogene%2C SopA-related%2C pentapeptide repeats-containing;Dbxref=ASAP:ABE-0013224,UniProtKB%2FSwiss-Prot:P32690,EcoGene:EG11927,GeneID:948546;gbkey=CDS;gene=yjbI;pseudo=true;transl_table=11                                         :   3  
 ID=cds1153;Parent=gene1190;Note=pseudogene;Dbxref=ASAP:ABE-0003933,ASAP:ABE-0285042,UniProtKB%2FSwiss-Prot:P76000,EcoGene:EG13890,GeneID:1450255;gbkey=CDS;gene=ycgI;pseudo=true;transl_table=11                                                                          :   2  
 ID=cds1302;Parent=gene1345;Note=pseudogene%7Eputative ATP-binding component of a transport system;Dbxref=ASAP:ABE-0004422,ASAP:ABE-0285045,UniProtKB%2FSwiss-Prot:P77481,EcoGene:EG13919,GeneID:4306141;gbkey=CDS;gene=ycjV;pseudo=true;transl_table=11                   :   2  
 (Other)                                                                                                                                                                                                                                                                   :9704  

How can we combine a FASTA file and a GFF file to get the gene sequences?

Write a function that combines a FASTA of the full genome and a GFF.

The output must be a FASTA file with the aminoacidic sequence of the coded proteins.

• What are the inputs?
• What is the output?
• What are the steps between them?

See write.fasta()

• What is a Transcription Factor (TF)?
• What is a Binding Site (BS)?

• Gene X codes for a Transcription Factor (TF)
• The TF attaches to DNA on binding sites (BS)
• This modifies the expression of genes A and B
• We say that X regulates A and B

Sigma 70 factor of E.coli binds to:

TTGACA-N(15-19)-TATAAT

What does this mean?

http://regulondb.ccg.unam.mx/

The most complete database of E.coli regulation

Look for Sigma Factor 70

See also: Downloads

Transcription Factor Dan has 5 binding sites in different parts of the genome.

The sequences are:

GTTAATT
GTGTATT
ATTCATT
GTTGATT
GTTAATT

How do we summrize this?

How to make an “average”? A model?

A string to represent many strings

GTTAATT
GTGTATT
ATTCATT        [GA]T[TG][ACTG]ATT
GTTGATT
GTTAATT

GTTAATT
GTGTATT
ATTCATT
GTTGATT
GTTAATT

A   |   1   0   0   2   5   0   0
C   |   0   0   0   1   0   0   0
G   |   4   0   1   1   0   0   0
T   |   0   5   4   1   0   5   5

Each column has different score. Total score is the sum of all

PSSM gives the Score of each position in the window

M[nucl,pos]

For each start position we evaluate the sum of the scores of the nucleotides in the window

Write a function to evaluate the score of a position for a given matrix

Inputs:

• pos: position in the genome
• genome: vector of chars
• mat: a position specific score matrix

Output: the score

Evaluate it on each position of E.coli genome.