EMBOSS

task 1 (Compile multiple .fasta files in one)

bench-mark data 1 bench-mark data 2 bench-mark data 3 bench-mark data 4

seqret "DRD*.fasta" DRD_ALL.fasta

Result

task 2 (Split .fasta file)

bench-mark data

seqretsplit  DRD_ALL.fasta

Result 1 Result 2 Result 3 Result 4

task 3 (Getting coding regions from .gb file)

bench-mark data

seqret coli.gb[275:3691]
seqret coli.gb[2756:3692:r]
seqret coli.gb[27566:28922]

Result 1 Result 2 Result 3

task 4 (Translation of sequences)

bench-mark data

transeq DRD1.fasta DRD1_tr.fasta -frame 1

Result 1

task 5 (Getting the orf's with minimal size)

bench-mark data

getorf DRD2.fasta -minsize 600

Result 1

task 6 (Translating the alignments in different formats)

bench-mark data

seqret pots.fasta msf::pots.msf

Result 1

task 8 (Translating the annotations from .gb to .gff)

bench-mark data

featcopy -features coli.gb -outfeat coli.gff

Result 1

task 9 (Getting the CDS from .gb file)

bench-mark data

extractfeat -type CDS coli.gb coli.fasta 

Result 1

task 10 (Shuffling sequences)

bench-mark data

shuffleseq -sequence DRD1.fasta -outseq DRD1_shuffled.fasta -shuffle 1

Result 1

task 11 (Making the random sequences)

makenucseq -amount 3 -length 100

Result 1

task 12 (Getting the codon frequency table)

bench-mark data

cusp ecoli.gb

Result 1

task 14 (Degapping the alignments)

bench-mark data

degapseq pots.fasta pots_degap.fasta

Result 1

task 15 (Changing the format of a carriage return symbols)

bench-mark data

noreturn DRD4.fasta DRD4.noreturn -system unix

Result 1

task 15 (Changing the format of the sra files)

bench-mark data

seqret sra_data.fastq fasta::sra_data.fasta

Result 1

task 3 (Comparing expected and observed frequencies in the bacterial genome)

script bench-mark data

The script takes the name of a .fasta file as a command line argument, and outputs expected and observed frequencies in a line: "The most differ dinucleotide is XY. The difference from expected value is 0.000000"

task 4 (Converting gb/embl files in fasta files with CDS and descriptions)

script bench-mark data 1 bench-mark data 2

The script takes the name of a .gb or .embl file (With different extensions error occurs), and creates the .fasta file with CDS.

---

© Gumerov Ruslan, 2017