Taur.vil Week 4

Week 4 Individual Journal

1)

• Code

cat infA-E.coli-K12.txt | sed "s/cat[at]at/ <-10box> & <\/-10box> /g" | sed "s/................. <-10box>/ <\/-35box> &/g" |sed "s/...... <\/-35box>/ <-35box> &/g" | sed "s/ <-10box> ...... <\/-10box> ...../& <tss> /g" | sed "s/ <tss> ./& <\/tss> /g" | sed "s/gagg/ <rbs> & <\/rbs>\n/g" | sed "2s/atg/ <start_codon> & <\/start_codon> /1" | sed -r "2s/<\/start_codon> .{3}*t[ag][ag]/& <\/stop_codon> /g" | sed "2s/... <\/stop_codon>/ <stop_codon> &/g" | sed "2s/aaaaggt/ <terminator> &/g" | sed "2s/tttt..../& <\/terminator> /2"

Question: how do you go about deleting a line break in program? To delete all the text spaces and the line break I had to go through manually and delete each one.

• Output

ttttcaccacaagaatgaatgttttcggcacatttctccccagagtgttataattgcggtcgcagagttggttacgctcattaccccgctgccgataaggaatttttcgcgtcaggtaacgcccatcgtttatctcaccgctcccttatacgttgcgcttttggtgcggcttagccgtgtgttttcggagtaatgtgccgaacctgtttgttgcgatttagcgcgcaaatc<-35box>tttact </-35box>tatttacagaacttcgg<-10box>cattat</-10box>cttgc<tss>c</tss>ggttcaaattacggtagtgatacccca<rbs>gagg</rbs>attag<start_codon>atg</start_codon>gccaaagaagacaatattgaaatgcaaggtaccgttcttgaaacgttgcctaataccatgttccgcgtagagttagaaaacggtcacgtggttactgcacacatctccggtaaaatgcgcaaaaactacatccgcatcctgacgggcgacaaagtgactgttgaactgaccccgtacgacctgagcaaaggccgcattgtcttccgtagtcgc<stop_codon>tga</stop_codon>ttgttttaccgcctgatgggcgaagagaaagaacgagt<terminator>aaaaggtcggtttaaccggcctttttatt</terminator>ttat

2)

By Tauras Vilgalys

As part of Biological Databases

Please Remember the Harassing of Deities is Strictly Prohibited

Never Forget Samson