MutAlign

Creating HTML visualizations of VESPA mutation effect predictions based on sequence alignments

This tool is useful, if you want to visually compare VESPA mutation effect predictions for highly similar sequences (e.g. the same protein in different organisms).

Requirements

MutAlign itself requires BioPython:

pip install biopython

Refer to the VESPA documentation for installation instructions. You will also need MMSeqs2 for sequence alignments.

Usage example

Let's say you are interested in a comparison of mutation effects in the POLK gene (DNA polymerase) in human and mice. Obtain the two amino-acid sequences and store them in POLK_HUMAN.fasta and POLK_MOUSE.fasta:

>POLK_HUMAN
MDSTKEKCDSYKDDLLLRMGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQV
NQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDN
PELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKE
VKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNK
LSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFR
IEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKV
TEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVER
TFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVST
AEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEEDRKHQQRSIIGFLQAGNQAL
SATECTLEKTDKDKFVKPLEMSHKKSFFDKKRSERKWSHQDTFKCEAVNKQSFQTSQPFQ
VLKKKMNENLEISENSDDCQILTCPVCFRAQGCISLEALNKHVDECLDGPSISENFKMFS
CSHVSATKVNKKENVPASSLCEKQDYEAHPKIKEISSVDCIALVDTIDNSSKAESIDALS
NKHSKEECSSLPSKSFNIEHCHQNSSSTVSLENEDVGSFRQEYRQPYLCEVKTGQALVCP
VCNVEQKTSDLTLFNVHVDVCLNKSFIQELRKDKFNPVNQPKESSRSTGSSSGVQKAVTR
TKRPGLMTKYSTSKKIKPNNPKHTLDIFFK

>POLK_MOUSE
MDNTKEKDNFKDDLLLRMGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVN
QRIENMMQQKAQITSQQLRKAQLQVDKFAMELERNRNLNNTIVHVDMDAFYAAVEMRDNP
ELKDKPIAVGSMSMLATSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEV
KEILAEYDPNFMAMSLDEAYLNITQHLQERQDWPEDKRRYFIKMGNYLKIDTPRQEANEL
TEYERSISPLLFEDSPPDLQPQGSPFQLNSEEQNNPQIAQNSVVFGTSAEEVVKEIRFRI
EQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPSRSAVMDFIKDLPIRKVSGIGKVT
EKMLMALGIVTCTELYQQRALLSLLFSETSWHYFLHIALGLGSTDLARDGERKSMSVERT
FSEISKTEEQYSLCQELCAELAHDLQKEGLKGRTVTIKLKNVNFEVKTRASTVPAAISTA
EEIFAIAKELLRTEVNVGSPHPLRLRLMGVRMSTFSSEDDRKHQQRSIIGFLQAGNQALS
STGDSLDKTDKTELAKPLEMSHKKSFFDKKRSERISNCQDTSRCKTAGQQALQILEPSQA
LKKLSESFETSENSNDCQTFICPVCFREQEGVSLEAFNEHVDECLDGPSTSENSKISCYS
HASSADIGQKEDVHPSIPLCEKRGHENGEITLVDGVDLTGTEDRSLKAARMDTLENNRSK
EECPDIPDKSCPISLENETISTLSRQDSVQPCTDEVVTGRALVCPVCNLEQETSDLTLFN
IHVDICLNKGIIQELRNSEGNSVKQPKESSRSTDRLQKASGRTKRPGTKTKSSTLKKTKP
RDPRHTLDGFFK

VESPA predictions

Run VESPA on the individual sequences and store the results in the directory vespa_predictions as the files POLK_HUMAN.csv and POLK_MOUSE.csv.

Sequence alignment

Use MMSeqs2 to align the sequences to each other:

mmseqs createdb POLK_HUMAN.fasta human
mmseqs createdb POLK_MOUSE.fasta mouse
mmseqs search human mouse result tmp
mmseqs result2msa human mouse result msa --msa-format-mode 6
head -n -1 msa > alignment_files/POLK.a3m

Tell MutAlign the alignments it should process

Put the name of the identifiers you want to process (here: POLK) into the file identifiers.txt:

cat POLK > identifiers.txt

The identifiers should correspond to alignment file names. Respectively, the sequence identifiers inside of the alignment files should correspond to the file names of the VESPA outputs from above.

Run MutAlign

python create_html.py

This will output HTML files in the directory ./html/. If you want a different output directory, you can specify it as a parameter to the MutAlign script, e.g.:

python create_html.py /home/johndoe/public_html/