Chromatin Immunoprecipitation Sequencing    ◾    247

streme --p chip3_peaks.fasta \

--oc streme_motifs_chip3 \

--dna \

--thresh 0.05

Each of the above commands will create a directory, “streme_motifs_*”. Four files will be

produced inside each directory: “sequences.tsv”, “streme.html”, “streme.txt”, and “streme.

xml”. Figure 6.20 shows how “streme.html” is displayed in the Internet browser.

TABLE 6.2  IUPAC Codes for DNA Alphabet

Nucleobase Name

IUPAC Symbol

Complement

Adenine

A

T

Cytosine

C

G

Guanine

G

C

Thymine

T U

A

Name

Symbol(s)

Matches

Any base

N . X

A C G T

Not T

V

A C G

Not G

H

A C T

Not C

D

A G T

Not A

B

C G T

Amino

M

A C

Purine

R

A G

Weak

W

A T

Strong

S

C G

Pyrimidine

Y

C T

Keto

K

G T

FIGURE 6.20  The motifs found by STREME.