Practical Work

Data extraction

a biologist provided you a compressed archive TP_DATAS.tar.gz

• extract archive to some place where you will work with.
• remove windows end of line of each files

Data filtering

• given the Q8I1R6-uniprot-blastp.m8 file
• extract the name of the 20 sequence that have the best percent of homology
• convert those 20 sequence to fasta using squizz

hint: blast m8 formated files display the following files

query, id, percent identity, alignment length, number of mismatches, number of gap openings, query start, query end, subject start, subject end, Expect value, HSP bit score separated by tabulation

Data Sorting

• get the number of different species that align with plasmodium Q8I1R6 dihydrofolate reductase
• sort sequence files according to the speciy they pertain (eg Toxoplasma sequence in a Toxoplasma folder, and so on)