EMBOSS

Tasks were done by EMBOSS 6.6.0.0 installed on kodomo.

Task 1

I need to join a few files in FASTA format into one. Files to combine: to_join. The result: joined.fasta.

Syntax (using seqret):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ seqret
Read and write (return) sequences
Input (gapped) sequence(s): to_join/*.fasta
output sequence(s) [3_cds_aac74892.fasta]: joined.fasta

Task 2

I need to split a files in FASTA format into a few different files. File to separate: coding3.fasta. The result: splited.

Syntax (using seqretsplit):

potanina.darya@kodomo:~/public_html/term3/block2/pr9/splited$ seqretsplit
Read sequences and write them to individual files
Input (gapped) sequence(s): ../to_split/coding3.fasta
output sequence(s) [3_cds_aac77347.fasta]:

Task 3

I need to cut from the chromosome (GB file) three coding sequence at the specified coordinates and save them in a single file in FASTA format. I used chromosome_1_yeast.gb - Saccharomyces cerevisiae S288C chromosome I and list3.txt - a list of coding sequences' coordinates. The result: 3_cod_seq.fasta.

Syntax (using seqret):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ seqret @list3.txt 3_cod_seq.fasta
Read and write (return) sequences

Task 4

I need to translate the coding sequences using a specific table of the genetic code. I used "table 11" - Bacterial. File to translate: gene_sequences.fasta. The result: translated4.fasta.

Syntax (using transeq):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ transeq -frame 1 -table 11 13/gene_sequences.fasta -outseq transla ted4.fasta
Translate nucleic acid sequences

Task 5

I need to translate the coding sequences with 6 different frames of translation. File to translate: coding.fasta. The result: translated5.fasta.

Syntax (using transeq):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ transeq -frame 6 coding.fasta -outseq translated5.fasta
Translate nucleic acid sequences

Task 6

I need to convert a file from FASTA format to MSF format. File contains alignment: alignment.fasta. The result: alignment.msf.

Syntax (using seqret):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ seqret alignment.fasta msf::alignment.msf
Read and write (return) sequences

Task 7

I need to write into file the number of matching letters between the second sequence alignment and all the rest. File contains alignment: alignment.fasta. The result: alignment7.

Syntax (using infoalign):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ infoalign -refseq 2 -only -name -idcount alignment.fasta alignment7
Display basic information about a multiple sequence alignment

Task 8

I need to convert the annotation features from the record in GB format to GFF format. I used chromosome_1_yeast.gb - Saccharomyces cerevisiae S288C chromosome. The result chromosome_1_yeast.gff.

Syntax (using featcopy):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ featcopy chromosome_1_yeast.gb chromosome_1_yeast.gff
Read and write a feature table

Task 9

I need to cut from the chromosome (GB file) coding sequences and save them in a single file in FASTA format. I used chromosome_1_yeast.gb - Saccharomyces cerevisiae S288C chromosome I. The result: cod_seqs.fasta.

Syntax (using extractfeat):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ extractfeat -type CDS chromosome_1_yeast.gb cod_seqs.fasta
Extract features from sequence(s)

Task 10

I need to shuffle the letters in a nucleotide sequence. I used coding.fasta. The result: shuffled.fasta.

Syntax (using shuffleseq):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ shuffleseq coding.fasta shuffled.fasta
Shuffle a set of sequences maintaining composition

Task 13

I need to find out the frequency of codons in coding sequences. I used cod_seqs.fasta. The result codon_freq.txt.

Syntax (using cusp):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ cusp cod_seqs.fasta codon_freq.txt
Create a codon usage table from nucleotide sequence(s)

Task 15

I need to align coding sequences in respectively the alignment of proteins. I used files from 13. The result: tranaligned.fasta.

Syntax (using tranalign):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ tranalign 13/gene_sequences.fasta 13/protein_alignment.fasta
Generate an alignment of nucleic coding regions from aligned proteins
(aligned) nucleotide output sequence set [1573620-1574456.fasta]: tranaligned.fasta

Task 17

I need to delete gaps and other extraneous characters from the alignment. I used: alignment.fasta. The result: alignment_processed.fasta.

Syntax (using degapseq):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ degapseq alignment.fasta alignment_processed.fasta
Remove non-alphabetic (e.g. gap) characters from sequences

Task 18

I need to convert the line endings to UNIX. I used: 17.txt. The result: 17_unix.txt.

Syntax (using noreturn):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ noreturn 17.txt 17_unix.txt
Remove carriage return from ASCII files

Task 19

I need to create 3 random sequences with 100 nucleotides. The result 19.fasta.

Syntax (using makenucseq):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ makenucseq -amount 3 -length 100 19.fasta
Create random nucleotide sequences
Codon usage file (optional):

Task 20

I need to convert file in FASTQ format to FASTA format. I used: sra_data.fastq. The result: sra_data.fasta.

Syntax (using seqret):

potanina.darya@kodomo:~/public_html/term3/block2/pr9$ seqret sra_data.fastq fasta::sra_data.fasta
Read and write (return) sequences

Term 3

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