Mini-Tutorals: Difference between revisions
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==bp-utils: bioseq== | ==bp-utils: bioseq== | ||
* Use accession "CP002316" to retrieve the Genbank file from NCBI. Save the output (in genbank format) to a file named as "cp002316.gb" | |||
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* 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. | |||
* Count the number of sequences | |||
* In a single command, pick the first 10 sequences and find their length | |||
* 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 | |||
* Find the base composition of the last two sequences | |||
* Pick the sequence with id "Bbu|D1_B11|8784|9302|1" and count the number of codons present in this sequence | |||
* Delete the last 10 sequences from the file and save the output to cp002316-v2.nuc | |||
* In a single command, pick the first sequence, then get the 50-110 nucleotides and make reverse complement of the sub-sequences | |||
* 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. | |||
Revision as of 21:38, 19 June 2015
bp-utils: bioseq
- 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- 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.
- Count the number of sequences
- In a single command, pick the first 10 sequences and find their length
- 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
- Find the base composition of the last two sequences
- Pick the sequence with id "Bbu|D1_B11|8784|9302|1" and count the number of codons present in this sequence
- Delete the last 10 sequences from the file and save the output to cp002316-v2.nuc
- In a single command, pick the first sequence, then get the 50-110 nucleotides and make reverse complement of the sub-sequences
- 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.