Mini-Tutorals

bp-utils: bioseq

1. Use accession "CP002316" to retrieve the Genbank file from NCBI. Save the output (in genbank format) to a file named as "cp002316.gb"

bioseq -f "CP002316.1" -o'genbank' > cp002316.gb

1. Use the above file as input, extract FASTA sequences for each genes and save the output to a new file called "cp002316.nuc". Use this file for the following questions.
2. Count the number of sequences
3. In a single command, pick the first 10 sequences and find their length
4. In a single command, pick the third and seventh sequences from the file and do the 3-frame translation. Which reading frame is the correct or both? Specify
5. Find the base composition of the last two sequences
6. Pick the sequence with id "Bbu|D1_B11|8784|9302|1" and count the number of codons present in this sequence
7. Delete the last 10 sequences from the file and save the output to cp002316-v2.nuc
8. In a single command, pick the first sequence, then get the 50-110 nucleotides and make reverse complement of the sub-sequences
9. In a single command, get the first 100 nucleotides of all the sequences present in the file and do 1-frame translation of all sub-sequences.