8 seqs/day

96 seqs/2 hrs

Bioinformatics for Genomics

TAGAGCATCGATCGATGCTGCAGATGATGCTAGCATCGGCTAGGCGACG

ATCTCGTAGCTA

ATCTCGTAGCTAGCTACGACGTCTA

ATCTCGTAGCTAGCTA

ATCTCGTAGCTAGATCTCGTAGCTAGCATCTCGTAGCTAGCT

ATCTCGTAGCTAGCTACATCTCGTAGCTAGCTACGATCTCGTAGCTAGCTACGAATCTCGTAGCTAGCTACGACATCTCGTAGCTAGCTACGACGATCTCGTAGCTAGCTACGACGTATCTCGTAGCTAGCTACGACGTCATCTCGTAGCTAGCTACGACGTCT

ATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCTATCTCGTAGCT

A

G

C

T

A

C

G

A

C

G

T

C

T

A

20

30

10

• Random base calling at the beggining or the end of read (Phred < 10)• Trimming (trim or trim_alt algorithms)

•Phred does the base calling

chromatogram

acgatctcgctagctgctactgtagccgcgattattcgcgatctacgtatatcgcgatcgatc

• Each base has assigned a chance of failure

• 1% = 0,01 = 10-2 = Phred 20

Base calling & trimming

Start

End

Goal: To document the presence of transcripts in a transcriptome [otorrin... in portuguese]

• EST = Expressed Sequence Tag

Partial sequencing of transcripts in EST genome projects

actgatcatctcgctgatgcgatc

work