Mini-Tutorals: Difference between revisions
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imported>Weigang (Created page with "==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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==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" | # Use accession "CP002316" to retrieve the Genbank file from NCBI. Save the output (in genbank format) to a file named as "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. | |||
Revision as of 17:47, 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"
- 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.