Multiple sequence alignment of Cas9 homologs

This script searches for proteins homologous to Cas9 from Streptococcus pyogenes via NCBI BLAST and performs a multiple sequence alignment of the hit sequences afterwards, using MUSCLE.

MSA results:
Q99ZW2     ---------------------MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSG--ETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENP------INASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDR---FNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRR-YTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGD--SLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQ--KNSRERMKRIEEGIKELGSQILKEH------PVENTQLQNEKLYLYYLQNGRDMYVDQELDINRL----SDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLIT-QRKFDNLTKAERGGLSELDKAG-------FIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIM--NFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQ-TGGFSKE----------SILPKRNSDKLIARKKD---WDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGIT----IMERSSFEKNPI-DFLEAKG-----YKEVKKDLIIKLPKYSLFELE----------NGRKRMLASA-------GELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENII--------HLFTLTNLGAPAAFKYFDTTIDRKR-YTSTKEVLDATLIHQSITGLYE--TRIDLSQLGGD
Q8DTE3     ---------------------MKKPYSIGLDIGTNSVGWAVVTDDYKVPAKKMKVLGNTDKSHIEKNLLGALLFDSG--NTAEDRRLKRTARRRYTRRRNRILYLQEIFSEEMGKVDDSFFHRLEDSFLVTEDKRGERHPIFGNLEEEVKYHENFPTIYHLRQYLADNPEKVDLRLVYLALAHIIKFRGHFLIEGKFDTRNNDVQRLFQEFLAVYDNTFENSS------LQEQNVQVEEILTDKISKSAKKDRVLKLFPNEKSNGRFAEFLKLIVGNQADFKKHFELEEKAPLQFSKDTYEEELEVLLAQIGDNYAELFLSAKKLYDSILLSGILTVTDVGTKAPLSASMIQRYNEHQMDLAQLKQFIRQKLSDKYNEVFSDVSKDGYAGYIDGKTNQEAFYKYLKGLLNKIEGSGYFLDKIEREDFLRKQRTFDNGSIPHQIHLQEMRAIIRRQAEFYPFLADNQDRIEKLLTFRIPYYVGPLARGKSDFAWLSRKSADKITPWNFDEIVDKESSAEAFINRMTNYDLYLPNQKVLPKHSLLYEKFTVYNELTKVKYKTE-QGKTAFFDANMKQEIFDGVFKVYRKVTKDKLMDFLEKEFDEFRIVDLTGLDKENKVFNASYGTYHDLCKIL-DKDFLDNSKNEKILEDIVLTLTLFEDREMIRKRLENYSDLLTKEQVKKLERRH-YTGWGRLSAELIHGIRNKESRKTILDYLIDDGNSNRNFMQLINDDALSFKEEIAKAQVIGETD--NLNQVVSDIAGSPAIKKGILQSLKIVDELVKIMG-HQPENIVVEMARENQFTNQGR--RNSQQRLKGLTDSIKEFGSQILKEH------PVENSQLQNDRLFLYYLQNGRDMYTGEELDIDYL----SQYDIDHIIPQAFIKDNSIDNRVLTSSKENRGKSDDVPSKDVVRKMKSYWSKLLSAKLIT-QRKFDNLTKAERGGLTDDDKAG-------FIKRQLVETRQITKHVARILDERFNTETDENNKKIRQVKIVTLKSNLVSNFRKEFELYKVREINDYHHAHDAYLNAVIGKALLGVYPQLEPEFVYGDYPHFHGHKE--------NKATAKKFFYSNIM--NFFKKD------DVRT-------DKNGEIIWKKDEHISNIKKVLSYPQVNIVKKVEEQ-TGGFSKE----------SILPKGNSDKLIPRKTKKFYWDTKKYGGFDSPIVAYSILVIADIEKGKSKKLKTVKALVGVT----IMEKMTFERDPV-AFLERKG-----YRNVQEENIIKLPKYSLFKLE----------NGRKRLLASA-------RELQKGNEIVLPNHLGTLLYHAKNIHKV-----DEPKHLDYVDKHKDEFKELLDVVSNFSKKYTLAEGNLEKIKELYAQNNGEDLKELASSFI--------NLLTFTAIGAPATFKFFDKNIDRKR-YTSTTEILNATLIHQSITGLYE--TRIDLNKLGGD
Q03JI6     ---------------------MTKPYSIGLDIGTNSVGWAVTTDNYKVPSKKMKVLGNTSKKYIKKNLLGVLLFDSG--ITAEGRRLKRTARRRYTRRRNRILYLQEIFSTEMATLDDAFFQRLDDSFLVPDDKRDSKYPIFGNLVEEKAYHDEFPTIYHLRKYLADSTKKADLRLVYLALAHMIKYRGHFLIEGEFNSKNNDIQKNFQDFLDTYNAIFESDL------SLENSKQLEEIVKDKISKLEKKDRILKLFPGEKNSGIFSEFLKLIVGNQADFRKCFNLDEKASLHFSKESYDEDLETLLGYIGDDYSDVFLKAKKLYDAILLSGFLTVTDNETEAPLSSAMIKRYNEHKEDLALLKEYIRNISLKTYNEVFKDDTKNGYAGYIDGKTNQEDFYVYLKKLLAEFEGADYFLEKIDREDFLRKQRTFDNGSIPYQIHLQEMRAILDKQAKFYPFLAKNKERIEKILTFRIPYYVGPLARGNSDFAWSIRKRNEKITPWNFEDVIDKESSAEAFINRMTSFDLYLPEEKVLPKHSLLYETFNVYNELTKVRFIAESMRDYQFLDSKQKKDIVRLYFKDKRKVTDKDIIE-YLHAIYGYDGIELKGIEKQ---FNSSLSTYHDLLNIINDKEFLDDSSNEAIIEEIIHTLTIFEDREMIKQRLSKFENIFDKSVLKKLSRRH-YTGWGKLSAKLINGIRDEKSGNTILDYLIDDGISNRNFMQLIHDDALSFKKKIQKAQIIGDEDKGNIKEVVKSLPGSPAIKKGILQSIKIVDELVKVMGGRKPESIVVEMARENQYTNQGK--SNSQQRLKRLEKSLKELGSKILKENIPAKLSKIDNNALQNDRLYLYYLQNGKDMYTGDDLDIDRL----SNYDIDHIIPQAFLKDNSIDNKVLVSSASNRGKSDDVPSLEVVKKRKTFWYQLLKSKLIS-QRKFDNLTKAERGGLSPEDKAG-------FIQRQLVETRQITKHVARLLDEKFNNKKDENNRAVRTVKIITLKSTLVSQFRKDFELYKVREINDFHHAHDAYLNAVVASALLKKYPKLEPEFVYGDYPKYNSFRE-------RKSATEKVYFYSNIM--NIFKKSISLADGRVIERPLIEVNEETGESVWNKESDLATVRRVLSYPQVNVVKKVEEQ-NHGLDRGKPKGLFNANLSSKPKPNSNENLVGAKE--YLDPKKYGGYAGISNSFTVLVKGTIEKGAKKKITNVLEFQGIS----ILDRINYRKDKL-NFLLEKG-----YKDI--ELIIELPKYSLFELS----------DGSRRMLASILSTNNKRGEIHKGNQIFLSQKFVKLLYHAKRISNT-----INENHRKYVENHKKEFEELFYYILEFNENYVGAKKNGKLLNSAFQSWQNHSIDELCSSFIGPTGSERKGLFELTSRGSAADFEFLGVKIPRYRDYTPSSLLKDATLIHQSVTGLYE--TRIDLAKLGEG
G3ECR1     MLFNKCIIISINLDFSNKEKCMTKPYSIGLDIGTNSVGWAVITDNYKVPSKKMKVLGNTSKKYIKKNLLGVLLFDSG--ITAEGRRLKRTARRRYTRRRNRILYLQEIFSTEMATLDDAFFQRLDDSFLVPDDKRDSKYPIFGNLVEEKVYHDEFPTIYHLRKYLADSTKKADLRLVYLALAHMIKYRGHFLIEGEFNSKNNDIQKNFQDFLDTYNAIFESDL------SLENSKQLEEIVKDKISKLEKKDRILKLFPGEKNSGIFSEFLKLIVGNQADFRKCFNLDEKASLHFSKESYDEDLETLLGYIGDDYSDVFLKAKKLYDAILLSGFLTVTDNETEAPLSSAMIKRYNEHKEDLALLKEYIRNISLKTYNEVFKDDTKNGYAGYIDGKTNQEDFYVYLKNLLAEFEGADYFLEKIDREDFLRKQRTFDNGSIPYQIHLQEMRAILDKQAKFYPFLAKNKERIEKILTFRIPYYVGPLARGNSDFAWSIRKRNEKITPWNFEDVIDKESSAEAFINRMTSFDLYLPEEKVLPKHSLLYETFNVYNELTKVRFIAESMRDYQFLDSKQKKDIVRLYFKDKRKVTDKDIIE-YLHAIYGYDGIELKGIEKQ---FNSSLSTYHDLLNIINDKEFLDDSSNEAIIEEIIHTLTIFEDREMIKQRLSKFENIFDKSVLKKLSRRH-YTGWGKLSAKLINGIRDEKSGNTILDYLIDDGISNRNFMQLIHDDALSFKKKIQKAQIIGDEDKGNIKEVVKSLPGSPAIKKGILQSIKIVDELVKVMGGRKPESIVVEMARENQYTNQGK--SNSQQRLKRLEKSLKELGSKILKENIPAKLSKIDNNALQNDRLYLYYLQNGKDMYTGDDLDIDRL----SNYDIDHIIPQAFLKDNSIDNKVLVSSASNRGKSDDFPSLEVVKKRKTFWYQLLKSKLIS-QRKFDNLTKAERGGLLPEDKAG-------FIQRQLVETRQITKHVARLLDEKFNNKKDENNRAVRTVKIITLKSTLVSQFRKDFELYKVREINDFHHAHDAYLNAVIASALLKKYPKLEPEFVYGDYPKYNSFRE-------RKSATEKVYFYSNIM--NIFKKSISLADGRVIERPLIEVNEETGESVWNKESDLATVRRVLSYPQVNVVKKVEEQ-NHGLDRGKPKGLFNANLSSKPKPNSNENLVGAKE--YLDPKKYGGYAGISNSFAVLVKGTIEKGAKKKITNVLEFQGIS----ILDRINYRKDKL-NFLLEKG-----YKDI--ELIIELPKYSLFELS----------DGSRRMLASILSTNNKRGEIHKGNQIFLSQKFVKLLYHAKRISNT-----INENHRKYVENHKKEFEELFYYILEFNENYVGAKKNGKLLNSAFQSWQNHSIDELCSSFIGPTGSERKGLFELTSRGSAADFEFLGVKIPRYRDYTPSSLLKDATLIHQSVTGLYE--TRIDLAKLGEG
Q927P4     ---------------------MKKPYTIGLDIGTNSVGWAVLTDQYDLVKRKMKIAGDSEKKQIKKNFWGVRLFDEG--QTAADRRMARTARRRIERRRNRISYLQGIFAEEMSKTDANFFCRLSDSFYVDNEKRNSRHPFFATIEEEVEYHKNYPTIYHLREELVNSSEKADLRLVYLALAHIIKYRGNFLIEGALDTQNTSVDGIYKQFIQTYNQVFASGIEDGSLKKLEDNKDVAKILVEKVTRKEKLERILKLYPGEKSAGMFAQFISLIVGSKGNFQKPFDLIEKSDIECAKDSYEEDLESLLALIGDEYAELFVAAKNAYSAVVLSSIITVAETETNAKLSASMIERFDTHEEDLGELKAFIKLHLPKHYEEIFSNTEKHGYAGYIDGKTKQADFYKYMKMTLENIEGADYFIAKIEKENFLRKQRTFDNGAIPHQLHLEELEAILHQQAKYYPFLKENYDKIKSLVTFRIPYFVGPLANGQSEFAWLTRKADGEIRPWNIEEKVDFGKSAVDFIEKMTNKDTYLPKENVLPKHSLCYQKYLVYNELTKVRYIND-QGKTSYFSGQEKEQIFNDLFKQKRKVKKKDL-ELFLRNMSHVESPTIEGLEDS---FNSSYSTYHDLLKVGIKQEILDNPVNTEMLENIVKILTVFEDKRMIKEQLQQFSDVLDGVVLKKLERRH-YTGWGRLSAKLLMGIRDKQSHLTILDYLMNDDGLNRNLMQLINDSNLSFKSIIEKEQVTTADK--DIQSIVADLAGSPAIKKGILQSLKIVDELVSVMG-YPPQTIVVEMARENQTTGKGK--NNSRPRYKSLEKAIKEFGSQILKEH------PTDNQELRNNRLYLYYLQNGKDMYTGQDLDIHNL----SNYDIDHIVPQSFITDNSIDNLVLTSSAGNREKGDDVPPLEIVRKRKVFWEKLYQGNLMS-KRKFDYLTKAERGGLTEADKAR-------FIHRQLVETRQITKNVANILHQRFNYEKDDHGNTMKQVRIVTLKSALVSQFRKQFQLYKVRDVNDYHHAHDAYLNGVVANTLLKVYPQLEPEFVYGDYHQFDWFKA--------NKATAKKQFYTNIM--LFFAQK-----DRII--------DENGEILWDK-KYLDTVKKVMSYRQMNIVKKTEIQ-KGEFSKA----------TIKPKGNSSKLIPRKTN---WDPMKYGGLDSPNMAYAVVI--EYAKGKNK-LVFEKKIIRVT----IMERKAFEKDEK-AFLEEQG-----YRQP--KVLAKLPKYTLYECE----------EGRRRMLASA-------NEAQKGNQQVLPNHLVTLLHHAANCEV------SDGKSLDYIESNREMFAELLAHVSEFAKRYTLAEANLNKINQLFEQNKEGDIKAIAQSFV--------DLMAFNAMGAPASFKFFETTIERKR-YNNLKELLNSTIIYQSITGLYE--SRKRLDD----
J7RUA5     ---------------------MKRNYILGLDIGITSVGYGII--DYE------------TRDVIDA---GVRLFKEANVENNEGRRSKRGARRLKRRRRHRIQRVKKLLFD---------YNLLTD-------------------------HSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHNVN-----------------------------------EVEEDTGNELSTKEQISRNSK-----------------------------------ALEEKYVAELQLERLKKD------------------------------------------------------------------------------------------GE---------VRGSINRFKTSDY---------------------------VKEAKQLLKVQKAYHQLDQSFIDTYIDLLETRRTYYEGP--GEGSPFGW------KDIKEW---------------YEMLMGHCTYFPEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYY---EKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTSTGKP---EFTNLKVYHDIKDITARKEIIENA---ELLDQIAKILTIYQSSEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDE------LWHTNDNQIAIFNRLKLVP----------KKVDLSQQKE--IPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYG--LPNDIIIELAREKNSKDAQKMINEMQKRNRQTNERIEE----IIRTT------GKENAKYLIEKIKLHDMQEGKCLYSLEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSFNNKVLVKQEENSKKGNRTPFQYLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEERDINRFSVQKDFINRNLVDTRYATRGLMNLLRSYFRVNNLD-------VKVKSINGGFTSFLRRKWKFKKERNKGYKHHAEDAL---IIANA----------DFIFKEWKKLDKAKK--------------------VMENQMFEEK------QAESMPEIETEQEYKEIFITP----HQIKHIKDFKDYKYSHRVDKKPNRELIND-------TLYSTRKDDKGNTLIVNNLN---------GLYDKDNDKLKKLI----NKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYE-------VNSKCYEEAKKLKKISNQAEFIASFYNNDLIKINGELYRVIGV----NNDLLNRIEVNMIDIT--YREYLENMNDKRPPRIIKTIASKTQSIKKYST-----------DILGNLYEVKSKKHPQIIKKG

# Code source: Patrick Kunzmann
# License: BSD 3 cl
from tempfile import gettempdir
import biotite.sequence as seq
import biotite.sequence.io.fasta as fasta
import biotite.sequence.graphics as graphics
import biotite.application.muscle as muscle
import biotite.application.blast as blast
import biotite.database.entrez as entrez
import matplotlib.pyplot as plt

# Download sequence of Streptococcus pyogenes Cas9
file_name = entrez.fetch("Q99ZW2", gettempdir(), "fa", "protein", "fasta")
fasta_file = fasta.FastaFile.read(file_name)
ref_seq = fasta.get_sequence(fasta_file)
# Find homologous proteins using NCBI Blast
# Search only the UniProt/SwissProt database
blast_app = blast.BlastWebApp("blastp", ref_seq, "swissprot", obey_rules=False)
blast_app.start()
blast_app.join()
alignments = blast_app.get_alignments()
# Get hit IDs for hits with score > 200
hits = []
for ali in alignments:
    if ali.score > 200:
        hits.append(ali.hit_id)
# Get the sequences from hit IDs
hit_seqs = []
for hit in hits:
    file_name = entrez.fetch(hit, gettempdir(), "fa", "protein", "fasta")
    fasta_file = fasta.FastaFile.read(file_name)
    hit_seqs.append(fasta.get_sequence(fasta_file))

# Perform a multiple sequence alignment using MUSCLE
app = muscle.MuscleApp(hit_seqs)
app.start()
app.join()
alignment = app.get_alignment()
# Print the MSA with hit IDs
print("MSA results:")
gapped_seqs = alignment.get_gapped_sequences()
for i in range(len(gapped_seqs)):
    print(hits[i], " "*3, gapped_seqs[i])

# Visualize the first 200 columns of the alignment
# Reorder alignments to reflect sequence distance

fig = plt.figure(figsize=(8.0, 8.0))
ax = fig.add_subplot(111)
order = app.get_alignment_order()
graphics.plot_alignment_type_based(
    ax, alignment[:200, order.tolist()], labels=[hits[i] for i in order],
    show_numbers=True, color_scheme="clustalx"
)
fig.tight_layout()

plt.show()