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Following exercises were fullfilled:
- Two fasta files TRNA.fasta, sequence1.fasta were combined in one final.fasta. Command: seqret @text.txt -outseq final.fasta
- One fasta file sequence1.fasta has been splited to several ones: seq1.fasta, seq2.fasta. Command: seqretsplit sequence1.fasta
- Translate this nucleotide sequence sequence2.fasta within six frames. Result: 3.fasta. Command: transeq -sequence sequence2.fasta -frame 6 -outseq 3.fasta
- Translate the alignment from .fasta format DNA.fasta to .msf format DNA.msf. Command: seqret DNA.fasta msf::DNA.msf
- Stir letters in a given nucleotide sequence TRNA.fasta. Result: 7.fasta. Command: shuffleseq TRNA.fasta -outseq 7.fasta
- Translate feature annotations in a .gb format entry chrom1.gb to the .gff table format. Result: 5.gff. Command: featcopy chrom1.gb -outfeat 5.gff
- Translate the coding sequences lying in one fasta file 1.fasta into amino acids using the specified table of the genetic code. The result is in one fasta file: 2.fasta. Command: transeq -table 0 -sequence 1.fasta -outseq 2.fasta
- From this file with chromosome in .gb format chrom2.gb get fasta file with coding sequences; add to the description of each sequence the function of the protein (from the product field). Result: 6.fasta. Command: extractfeat chrom2.gb -type CDS -describe product -outseq 6.fasta
- Extradite to the output stream the number of matching letters between the second alignment sequence 4.fasta and all the others (only the name of the sequence and the number are output). Result: 4.infoalign. Command: infoalign 4.fasta -refseq 2 -only -name -idcount
- From a file with a chromosome in the .gb format text2.txt, GB cut three coding sequences from the specified coordinates "from", "to", "orientation" and save in one fasta file. Result: 1.fasta. Command: seqret @text2.txt -outseq 1.fasta
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