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How to generate pairwise sequence alignments

This recipe produces pairwise alignments with different algorithms.

2 results • updated 5.1 years ago by Istvan Albert

This recipe produces pairwise alignments with different algorithms.

Sequence alignment is a mathematically well-defined concept - but there are different software alternatives to perform the operation and even more way to report the results.

For more information see the

Bioinformatics Data Analysis oline course
Biostar Handbook for system setup and other information.

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# Stop script on any error.
set -uex

# The default values will be comparing
# the Ebola strain from 1972 to one strain observed in 2014.
#
# Ebola virus Mayinga 1972: AF086833
# Ebola virus Makona 2014: KR105328

# Accession numbers for the two sequences that are to be aligned.
SEQ1=AF086833
SEQ2=KR105328

# Download sequences by accession numbers
efetch -db nuccore -format fasta -id $SEQ1 > $SEQ1.fa
efetch -db nuccore -format fasta -id $SEQ2 > $SEQ2.fa

#
# Typically you want to know what the scoring matrix is.
#
#
# Get the scoring matrix.
#
wget -q -nc ftp://ftp.ncbi.nlm.nih.gov/blast/matrices/NUC.4.4

# Global alignments.

# Using the default format.
echo "Tool:stretcher format:default(markx0)  file:alignment.1.txt "
stretcher -filter -asequence $SEQ1.fa -bsequence $SEQ2.fa -data NUC.4.4 > alignment.1.txt

#
# The stretcher has the NUC4.4 matrix built into it under the special
# name of EDNAFULL. From now on we will use that.
#

# Generate alignment in the so called markx2 format.
echo "Tool:stretcher format:markx2 file:alignment.2.txt"
stretcher -filter -asequence $SEQ1.fa -bsequence $SEQ2.fa  -data EDNAFULL -aformat markx2  > alignment.2.txt


# Generate alignment in the SAM format.
echo "Tool:stretcher format:SAM file:alignment.3.txt"
stretcher -filter -asequence $SEQ1.fa -bsequence $SEQ2.fa -data EDNAFULL -aformat sam > alignment.3.txt


#
# Local alignments.
#
# Generate a pariwise local alignment with blastn.
# It is surprisingly difficult to tell what scoring matrix
# blastn used. See blastn --help for information.
#

# The default output format of blasn.
echo "Tool:blastn format:blast file:alignment.4.txt"
blastn -subject $SEQ1.fa -query $SEQ2.fa > alignment.4.txt

# Format alignments in tabular form.
echo "Tool:blastn format:column file:alignment.5.txt"
blastn -subject $SEQ1.fa -query $SEQ2.fa -outfmt 7 > alignment.5.txt

#
# Semi global alignment.
#
# minimap2 configured to produces SAM format.
echo "Tool:minimap format:SAM file:alignment.6.txt"
minimap2 -a -x sr --eqx $SEQ1.fa $SEQ2.fa > alignment.6.txt

# minimap2 configured to produces PAF with MD tags.
echo "Tool:minimap format:PAF (MD) file:alignment.7.txt"
minimap2 -c --MD $SEQ1.fa $SEQ2.fa > alignment.7.txt

# minimap2 configured to produces OAF with CS tags.
echo "Tool:minimap format:PAF (CS) file:alignment.8.txt"
minimap2 --cs $SEQ1.fa $SEQ2.fa > alignment.8.txt

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[seq1]
label = "Accession number for the first sequence"
display = "TEXTBOX"
value = "AF086833"
help = "Must be an NCBI accession number"

[seq2]
label = "Accession number for the second sequence"
display = "TEXTBOX"
value = "KR105328"
help = "Must be an NCBI accession number"

[settings]
id = 77
recipe_uid = "recipe-align1"
uid = "recipe-align1"
name = "How to generate pairwise sequence alignments"
template = "How_to_generate_pairwise_sequence_alignments_bio-data-analysis_77.sh"
image = "How_to_generate_pairwise_sequence_alignments_bio-data-analysis_77.png"
project_uid = "bio-data-analysis"
url = "http://localhost8000"
help = "This recipe produces pairwise alignments with different algorithms.\n\nSequence alignment is a mathematically well-defined concept - but there are  different software alternatives to perform the operation and even more way to report the results. \n\nFor more information see the \n\n* [Bioinformatics Data Analysis][link] oline course\n* [Biostar Handbook][book] for system setup and other information.\n\n[link]: https://www.biostarhandbook.com/edu/course/4/\n[book]: https://www.biostarhandbook.com/"

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