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" | * Use accession "CP002316.1" to retrieve the Genbank file from NCBI. Save the output (in genbank format) to a file named as "cp002316.gb". | ||
<div class="toccolours mw-collapsible"> | <div class="toccolours mw-collapsible"> | ||
<syntaxhighlight lang=bash"> | <syntaxhighlight lang=bash"> | ||
| Line 7: | Line 7: | ||
</div> | </div> | ||
* 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 | <div class="toccolours mw-collapsible"> | ||
<syntaxhighlight lang=bash"> | |||
bioseq -i "genbank" -F cp002316.gb > cp002316.fas | |||
</syntaxhighlight> | |||
</div> | |||
* Count the number of sequences. | |||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioseq -n cp002316.fas | |||
</syntaxhighlight> | |||
</div> | |||
* 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 | <div class="toccolours mw-collapsible"> | ||
<syntaxhighlight lang=bash"> | |||
bioseq -p "order:1-10" cp002316.fas | bioseq –l | |||
</syntaxhighlight> | |||
</div> | |||
* 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 on both? Specify | |||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioseq -p "order:3,7" cp002316.fas | bioseq -t3 | |||
</syntaxhighlight> | |||
</div> | |||
* Find the base composition of the last two sequences | * Find the base composition of the last two sequences | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioseq -p "order:25-26" cp002316.fas| bioseq –c | |||
</syntaxhighlight> | |||
</div> | |||
* 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 | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioseq -p "id:BbuJD1_B11|8784|9302|1" cp002316.fas | bioseq –C | |||
</syntaxhighlight> | |||
</div> | |||
* 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 | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioseq -d "order:17-26" cp002316.fas > cp002316-v2.nuc | |||
</syntaxhighlight> | |||
</div> | |||
* 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 | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioseq -p "order:1" cp002316.fas | bioseq -s "50,110" | bioseq –r | |||
</syntaxhighlight> | |||
</div> | |||
* 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. | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioseq -s "1,50" cp002316.fas | bioseq -t1 | |||
</syntaxhighlight> | |||
</div> | |||
Revision as of 22:01, 19 June 2015
bp-utils: bioseq
- Use accession "CP002316.1" 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.
bioseq -i "genbank" -F cp002316.gb > cp002316.fas- Count the number of sequences.
bioseq -n cp002316.fas- In a single command, pick the first 10 sequences and find their length
bioseq -p "order:1-10" cp002316.fas | bioseq –l- 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 on both? Specify
bioseq -p "order:3,7" cp002316.fas | bioseq -t3- Find the base composition of the last two sequences
bioseq -p "order:25-26" cp002316.fas| bioseq –c- Pick the sequence with id "Bbu|D1_B11|8784|9302|1" and count the number of codons present in this sequence
bioseq -p "id:BbuJD1_B11|8784|9302|1" cp002316.fas | bioseq –C- Delete the last 10 sequences from the file and save the output to cp002316-v2.nuc
bioseq -d "order:17-26" cp002316.fas > 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
bioseq -p "order:1" cp002316.fas | bioseq -s "50,110" | bioseq –r- 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.
bioseq -s "1,50" cp002316.fas | bioseq -t1