Mini-Tutorals: Difference between revisions
Jump to navigation
Jump to search
imported>Weigang mNo edit summary |
imported>Saymon |
||
| Line 64: | Line 64: | ||
==bioaln: alignment/CLUSTALW manipulations== | ==bioaln: alignment/CLUSTALW manipulations== | ||
*Go to '''/home/shared/LabMeetingReadings/Test-Data''' and find the sequence alignment file “'''bioaln_tutorial.aln'''”. Name the format of the alignment file. Use it to answer all the questions below. | *Go to '''/home/shared/LabMeetingReadings/Test-Data''' and find the sequence alignment file “'''bioaln_tutorial.aln'''”. Name the format of the alignment file. Use it to answer all the questions below. | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
CLUSTALW | |||
</syntaxhighlight> | |||
</div> | |||
*Find the length of the alignment. | *Find the length of the alignment. | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioaln -l bioaln_tutorial.aln | |||
</syntaxhighlight> | |||
</div> | |||
*Count the number of the sequences present in the alignment. | *Count the number of the sequences present in the alignment. | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioaln -n bioaln_tutorial.aln | |||
</syntaxhighlight> | |||
</div> | |||
*How do you convert this alignment in phylip format? Save the output. | *How do you convert this alignment in phylip format? Save the output. | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioaln -o "phylip" bioaln_tutorial.aln > test.phy | |||
</syntaxhighlight> | |||
</div> | |||
*Pick “seq2, seq5, seq7, seq10” from the alignment and calculate their average percent identity. | *Pick “seq2, seq5, seq7, seq10” from the alignment and calculate their average percent identity. | ||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioaln -p "seq2, seq5, seq7, seq10" bioaln_tutorial.aln | bioaln -a | |||
</syntaxhighlight> | |||
</div> | |||
*Get an alignment slice from “50-140” and find the average identities of the slice for sliding windows of 25. | *Get an alignment slice from “50-140” and find the average identities of the slice for sliding windows of 25. | ||
*Extract conserved blocks from the alignment. | <div class="toccolours mw-collapsible"> | ||
<syntaxhighlight lang=bash"> | |||
bioaln -s "50, 140" bioaln_tutorial.aln | bioaln -w "25" | |||
</syntaxhighlight> | |||
</div> | |||
*Extract conserved blocks from the alignment. | |||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioaln -B bioaln_tutorial.aln | |||
</syntaxhighlight> | |||
</div> | |||
*Find the unique sequences and list their ids. | *Find the unique sequences and list their ids. | ||
*Extract third sites from the alignment and show only variable sites in match view. | <div class="toccolours mw-collapsible"> | ||
<syntaxhighlight lang=bash"> | |||
bioaln -u bioaln_tutorial.aln | bioaln -L | |||
</syntaxhighlight> | |||
</div> | |||
*Extract third sites from the alignment and show only variable sites in match view. | |||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioaln -T bioaln_tutorial.aln | bioaln -v | bioaln -m | |||
</syntaxhighlight> | |||
</div> | |||
*Remove the gaps and show the final alignment in codon view for an alignment slice “1-100”. | *Remove the gaps and show the final alignment in codon view for an alignment slice “1-100”. | ||
*Add a 90% consensus sequence and then show the final alignment in match plus codon view for an alignment slice “20-80”. (Hint: | <div class="toccolours mw-collapsible"> | ||
<syntaxhighlight lang=bash"> | |||
bioaln -s "1, 100" bioaln_tutorial.aln | bioaln -g | bioaln -c | |||
</syntaxhighlight> | |||
</div> | |||
*Add a 90% consensus sequence and then show the final alignment in match plus codon view for an alignment slice “20-80”. (Hint: match view followed by codon view) | |||
<div class="toccolours mw-collapsible"> | |||
<syntaxhighlight lang=bash"> | |||
bioaln -s "20, 80" bioaln_tutorial.aln | bioaln -C "90" | bioaln -m | bioaln -c | |||
</syntaxhighlight> | |||
</div> | |||
==biotree: tree/NEWICK manipulations== | ==biotree: tree/NEWICK manipulations== | ||
Revision as of 21:41, 2 July 2015
Bp-utils: sequence, alignment & tree utilities by Qiu Lab
bioseq: sequence/FASTA manipulations
- 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 "1,100" cp002316.fas | bioseq -t1bioaln: alignment/CLUSTALW manipulations
- Go to /home/shared/LabMeetingReadings/Test-Data and find the sequence alignment file “bioaln_tutorial.aln”. Name the format of the alignment file. Use it to answer all the questions below.
CLUSTALW- Find the length of the alignment.
bioaln -l bioaln_tutorial.aln- Count the number of the sequences present in the alignment.
bioaln -n bioaln_tutorial.aln- How do you convert this alignment in phylip format? Save the output.
bioaln -o "phylip" bioaln_tutorial.aln > test.phy- Pick “seq2, seq5, seq7, seq10” from the alignment and calculate their average percent identity.
bioaln -p "seq2, seq5, seq7, seq10" bioaln_tutorial.aln | bioaln -a- Get an alignment slice from “50-140” and find the average identities of the slice for sliding windows of 25.
bioaln -s "50, 140" bioaln_tutorial.aln | bioaln -w "25"- Extract conserved blocks from the alignment.
bioaln -B bioaln_tutorial.aln- Find the unique sequences and list their ids.
bioaln -u bioaln_tutorial.aln | bioaln -L- Extract third sites from the alignment and show only variable sites in match view.
bioaln -T bioaln_tutorial.aln | bioaln -v | bioaln -m- Remove the gaps and show the final alignment in codon view for an alignment slice “1-100”.
bioaln -s "1, 100" bioaln_tutorial.aln | bioaln -g | bioaln -c- Add a 90% consensus sequence and then show the final alignment in match plus codon view for an alignment slice “20-80”. (Hint: match view followed by codon view)
bioaln -s "20, 80" bioaln_tutorial.aln | bioaln -C "90" | bioaln -m | bioaln -c