Genomika: analýza a algoritmy - Cvičení 1

For english speaking students: I am sorry, I did not have time to translate it, but google translator (or any) and Marharyta will help yoy.

Připravit si základní sadu programů. Budeme je používat během celého semestru a budou se vám hodit během celé kariéry, připravte si je dobře:

• reformat_DNA; (reformat_AA): přeformátujte soubor s DNA (AA) na fasta formát. Program by měl vymazat všechny znaky mimo IUB kódů pro DNA nebo aminokyseliny. (mm_pax6-plain.txt)
• reverse_complement: fasta formát na vstupu převede na fasta druhého vlákna (výstup z reformat_DNA)
• statistic_DNA; (statistic_AA): základní statistika fasta filu (délka sekvence, ACGT složení, nejasné báze, kontrolní součet) (výstup z reformat_DNA a porovnat s mm_pax6.fasta)
• get_region: z fasta filu vystřihne zadanou oblast (z mm_pax6.fasta vystřihnout oblast 286-1596, uložit jako mm_pax6_cds.fasta)
• translate: přeložit DNA do proteinu (z mm_pax6_cds.fasta, uložit jako mm_pax6_aa.fasta )

Nejlépe by měly programy číst ze standardního vstupu a tamtéž poslat výstup. Tak, aby bylo možno použít konstrukce podobné těmto:

cat mm_pax6-plain.txt | reformat_DNA | statistic_DNA
cat mm_pax6.fasta | get_region 286 1596 | translate >mm_pax6_cds.aa

Příští týden zjistíme, kdo napsal programy nejlépe a ty se stanou naším zlatým standardem, tak do toho.

Data

Genetic code

Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
AAs    = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
	
Standard Code = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Vertebrate Mitochondrial Code = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
Yeast Mitochondrial Code = FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma Code = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Invertebrate Mitochondrial Code = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
Ciliate, Dasycladacean and Hexamita Nuclear Code = FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Echinoderm and Flatworm Mitochondrial Code = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Euplotid Nuclear Code = FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Bacterial, Archaeal and Plant Plastid Code = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Alternative Yeast Nuclear Code = FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Ascidian Mitochondrial Code = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
Alternative Flatworm Mitochondrial Code = FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Blepharisma Nuclear Code = FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Chlorophycean Mitochondrial Code = FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Trematode Mitochondrial Code = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Scenedesmus obliquus mitochondrial Code = FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Thraustochytrium Mitochondrial Code = FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Pterobranchia mitochondrial code = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG
Candidate Division SR1 and Gracilibacteria Code = FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
      

IUB Nucleotide Codes

Files:

• eco_laci.fasta
• eco_laci.gbk
• mm_pax6-ft.txt
• mm_pax6-plain.txt
• mm_pax6.fasta
• mm_pax6.gff3