Mini-Tutorals: Difference between revisions

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imported>Saymon
imported>Saymon
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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"
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<div class="toccolours mw-collapsible">
<syntaxhighlight lang=bash">
<syntaxhighlight lang=bash">
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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.
* 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
* Count the number of sequences
# In a single command, pick the first 10 sequences and find their length
* 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
* 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
* 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
* 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
* 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, 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.
* 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.