EMBOSS

Task 1. Combine fasta files

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/to_join/
Command line:
```
seqret "*.fasta"
```
Result: ↓

Task 2. Split the fasta file

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/to_split/coding1.fasta
Command line:
```
seqretsplit coding1.fasta
```
Result: ↓ (All u00096 files)

Task 3. Receive 3 sequence regions from .gb and write them together in .fasta

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/chromosome.gb + text file
Command line:
```
seqret @3.txt res3.fasta
```
Result: ↓

Task 4. Translate coding sequences to amino acid sequences. Save all in one fasta file

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/to_split/coding2.fasta
Command line:
```
transeq coding2.fasta -out res4.fasta
```
Result: ↓

Task 5. Translate given sequence in 6 reading frames

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/to_split/coding3.fasta

Command line:

transeq coding3.fasta -frame=6 -out res5.fasta

Result: ↓

Task 6. Translate alignment from .fasta to .msf

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/protein_alignment.fasta

Command line:

 seqret protein_alignment.fasta -outseq protein_alignment.msf

Result: ↓

Task 7. Compare second sequence in alignment file with the others. Display only name and number

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/protein_alignment.fasta

Command line:

infoalign fasta::protein_alignment.msf:RL2_RHIEC -only -name -idcount

Result:
```
RL2_RHIEC     278
```

Task 8. Translate annotations from .gb to .gff

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/chromosome.gb
Command line:
```
featcopy chromosome.gb chromosome.gff
```
Result: ↓

Task 9. Receive .fasta from .gb

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/chr.gb
Command line:
```
extractfeat chr.gb -out res9.fasta
```
Result: ↓

Task 10. Mix letters in nucleotide sequence

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/to_join/3.fasta
Command line:
```
shuffle 3.fasta
```

Result:

            >lcl|U00096.3_cds_AAC74887.1_1808 [gene=manX] [protein=fused mannose-specific PTS enzymes: IIA component/IIB component] [protein_id=AAC74887.1] [location=1902048
            AGTGTCACTCGATCCGCGTTAAGTGGTGCGACCAGAAACCTGATGAACAG
            CGTGTCGTTGCCGCATCCACCACGTCTGACGGAAGAACTACGATAAAAAG
            AATTACACGGGTTGTTGACCGACATGTGGCGTAAAGGCGTACACGGCGAG
            GCGCAGAGCAAGAGTCTCGAGAGTGGATGATGCGAAAAGAGCTCACACCG
            GAGCGCCAGGTATATTGGATCTACGCGAACAATGAATGGGCAGTCGCGAG
            ATAGACAGCATAGGTATGCGCATGTACGAAGCCAAACACTCCCGAGTGTA
            GTCAAGCCACGCATTCGGTGGTAGAACGTCCGCATCACCGTCCAGATCGC
            CATAGGAACACTGTTAAACACTGTATAGACATCCACACGACACATGAGCT
            GGGTCGGTCAAAACCATGTCTCTGGCCTAAATTAGATACACGAACAGCGG
            CGTGTAGGGGTCAGGTACGGCCCTGGCTCAGACCAAGATCGTTAGTGATT
            ATCAGCCGGCGGCCGGTTTTTTCGTTGGGAGCTCGGACTTCATGAACGGT
            TGCATGACAGGGAATGGAGTGTGTTAATTGCCCGTCTCCGGATCATGATA
            GGTCGAGCCACGTAATCCTTTGTTGTCATTTAATCACTCTCTCCTGCAAC
            CATTTTAATCCTCAATGATAGAGCGGCACGGTTTTTCCTTGACCTAGCAG
            GGCCATATTATGGCGAGGTCCACATGAACGGAATTGATGTGTGATCTAGG
            CAACCCCGTTGGGAAGGCATCGATAGTAGTCCCCACGTCCCAAGCGGGCA
            TATGTAGACGATAAAACGAAAGGGATCAAAGAAAGAACCACACAGTGGCC
            GAACTCCCAAGAAGCCTTTTGTCTAAATACATTAAGCCGCCTGTACATAG
            TTTATGTAACAACTGCAACGAGGACCCCATACTAGAAGCTACATCGGTTG
            GGGGTATGAGTGACAGAATTGT

Task 13. Receive codon freqeuncy from .fasta

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/to_split/coding1.fasta
Command line:
```
cusp coding1.fasta
```
Result: ↓

Task 15. Generate an alignment of nucleic coding regions from aligned proteins

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/to_split/coding2.fasta

Command line:

tranalign coding2.fasta res4.fasta -out res15.fasta

Result: ↓

Task 17. Remove non-alphabetic (e.g. gap) characters from .fasta

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/alignment.fasta
Command line:
```
degapseq alignment.fasta res17.fasta
```
Result: ↓

Task 18. Remove carriage return

Given data was here: 3.txt
Command line:
```
noreturn 3.txt res18.txt
```
Result: ↓

Task 19. Make 3 random sequences with the 100 nucleotides length

Given data: none

Command line:

 makenucseq -length 100 -amount 3  -auto res19.fasta

Result: ↓

Task 20. Translate .fastq to .fasta

Given data was here: http://kodomo.fbb.msu.ru/~sophia.veselova/term3/block2/pr9/sra_data.fastq

Command line:

 seqret sra_data.fastq -outseq res20.fasta

Result: ↓

Back to term 3 page 🚶