调整 MAFFT 命令行算法以更好地弥补差距
Adjusting the MAFFT command line algorithm to better account for gaps
我一直在尝试使用 MAFFT 命令行工具来识别基因组中的编码区域。我的一般过程是将基因的氨基酸共有序列与目标序列的翻译阅读框进行比对。我的方法在很大程度上是成功的。但是，我注意到一些奇怪的对齐方式，不幸的是它们会妨碍我的注释方法。下面是一个这样的例子（注意——我还包括了来自 Pairwise2 Biopython 模块的成对比对来演示我想要的输出。不幸的是，Pairwise2 的计算时间比 MAFFT 命令行慢了近 20 倍）：
from time import *
from Bio.SubsMat import MatrixInfo as matlist
from Bio import pairwise2
from Bio.pairwise2 import format_alignment
from Bio.Align.Applications import MafftCommandline
startTime = time()
sample_tList = [['>Frame 1', 'RIGVGSIPRHLYCQELPLAQPKTCCAETPFRDSPLQGRLGVCPHLASGVALLYGLSTPLTMSGILDRCTCTPNARVFMAEGQVYCTRCLSARSLLPLNLQVPELGVLGLFYRPEEPLRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPAVLKVLQVYERGCRWYPIVGPVPGVGVYANSLHVSDKPFPGATHVLTNLPLPQRPKPEDFCPFECAMADVYDIGHGAVMFVAGGKVSWAPRGGDEVRFETVPEELKLIANRLHISFPPHHLVDMSKFAFIVPGSGVSLRVEHQHGCLPADIVPKGNCWWCLFDLLPPGVQNREIRYANQFGYQTKHGVSGKYLQRRLQINGLRAVTDTHGPIVVQYFSVKESWIRHFRLAGEPSLPGFEDLLRIRVESNTSPLADKDEKIFRFGSHKWYGAGKRARKARSGATTTVAHRASSARETRQAKKHEGVDANNAAHLEHYSPPAEGNCGWHCISAIVNRMVNSNFETTLPERVRPSDDWATDEDFVNTIQILRLPAALDRNGACKSAKYVLKLEGEHWTVSVAPGMSPSLLPLECVQGCCEHKGGLGSPDAVEVSGFDPTCLDRLAEVMHLPSSVIPAALAEMSNNSDRPASLVNTAWTVSQFYARHTGGNHRDQVRLGKIISLCQVIEECCCHQNKTNRATPEEVAAKIDQYLRGATSLEECLIKLERVSPPSAADTSFDWNVVLPGVEAAGPTTEQPHANQCCAPVPVVTQEPLDKDSVPLTAFSLSNCYYPAQGDEVRHRERLNSVLSKLEEVVLEEYGLMPTGLGPRPVLPSGLDELKDQMEEDLLKLANAQATSEMMALAAEQVDLKAWVKSYPRWIPPPPPPKVQPRRMKPVKSLPENKPVPAPRRKVRSDPGKSILAVGGPLNFSTPSELVTPLGEPVLMPASQHVSRPVTPLSEPAPVPAPRRIVSRPMTPLSEPTFVFAPWRKSQQVEEANPAAATLTCQDEPLDLSASSQTEYEAYPLAPLENIGVLEAGGQEAEEVLSGISDILDNTNPAPVSSSSSLSSVKITRPKYSAQAIIDSGGPCSGHLQKEKEACLRIMREACDAARLGDPATQEWLSHMWDRVDVLTWRNTSVYQAFRTLDGRFGFLPKMILETPPPYPCGFVMLPHTPTPSVSAESDLTIGSVATEDVPRILGKTENTGNVLNQKPLALFEEEPVCDQPAKDSRTLSRESGDSTTAPPVGTGGAGLPTDLPPLDGVDADGGGLLRTAKGKAERFFDQLSRQVFNIVSHLPVFFSHLFKSDSGYSPGDWGFAAFTLFCLFLCYSYPFFGFAPLLGVFSGSSRRVRMGVFGCWLAFAVGLFKPVSDPVGAACEFDSPECRNILHSFELLKPWDPVRSLVVGPVGLGLAILGRLLGGARYIWHFLLRLGIVADCILAGAYVLSQGRCKKCWGSCIRTAPNEIAFNVFPFTRATRSSLIDLCDRFCAPKGMDPIFLATGWRGCWTGQSPIEQPSEKPIAFAQLDEKRITARTVVSQPYDPNQAVKCLRVLQAGGAMVAEAVPKVVKVSAIPFRAPFFPTGVKVDPECRIVVDPDTFTTALRSGYSTTNLVLGVGDFAQLNGLKIRQISKPSGGGPHLIAALHVACSMVLHMLAGVYVTAVGSCGTGTSDPWCANPFAVPGYGPGSLCTSRLCISQHGLTLPLTALVAGFGLQEIALVVLIFVSIGGMAHRLSCKADMLCILLAIASYVWVPLTWLLCVFPCWLRWFSLHPLTILWLVFFLISVNMPSGILAVVLLVSLWLLGRYTNIAGLVTPYDIHHYTSGPRGVAALATAPDGTYLAAVRRAALTGRTMLFTPSQLGSLLEGAFRTRKPSLNTVNVVGSSMGSGGVFTIDGRIKCVTAAHVLTGNSARVSGVGFNQMLDFDVKGDFAIADCPNWQGVAPKTQFCGDGWTGRAYWLTSSGVEPGVIGDGFAFCFTACGDSGSPVITEAGELVGVHTGSNKQGGGIVTRPSGQFCNVTPIKLSELSEFFAGPKVPLGDVKVGSHIIKDTSEVPSDLCALLAAKPELEGGLSTVQLLCVFFLLWRMMGHAWTPLVAVGFFILNEVLPAVLVRSVFSFGMFALSWLTPWSAQVLMIRLLTAALNRNRVSLIFYSLGAVTGFVADLATTQGHPLQAVMNLSTYAFLPRMMVVTSPVPAIACGVVHLLAIILYLFKYRCLHHVLVGDGAFSAAFFLRYFAEGKLREGVSQSCGMSHESLTGALAIKLSDEDLDFLTKWTDFKCFVSASNMRNAAGQFIEAAYAKALRIELAQLVQVDKVRGTLAKLEAFADTVAPQLSPGDIVVALGHTPVGSIFDLKVGSTKHTLQAIETRVLAGSKMTVARVVDPTPAPPPAPVPIPLPPKVLENGPNAWGGEDRLNKRKRRRMEAVGIFVMDGKKYQKFWDKNSGDVFYEEVHNSTDEWECLRAGDPADFDPETGIQCGHVTIEDKVYNVFTSPSGRRFLVPANPENRRIQWEAARLSVEQALGMMNVDGELTAKELEKLKRIIDKLQGLTKEQCLNCPPVAPAVVAAAWLLLRQRKNFTTGPSPDLTKWPVRLSRTRSSTTNIRLPNRLMVVLCSCAPLFLRLMSSPALMHLLSYLPATGRETLGLMARFGILRPRPPKRKSHLVRKYRLVTLGAVTHLKLVSLISCTLLGATLSGKEFYRIQGLETYLTEPPVTLEAQCMRLPASRPMLLRLMGVPSWPQPCPPVLSCMYRPFQRPSLIILILGLTALNSQSTVVRMLLGTSPNTICPPKALFCLEFFALCGSTCLPMWVSARPFIGLPLTLPRILWLEMGTDFQPRIFRASLKSTFCAHRLCEKTGKLLLLVPSRSSIVGRRRLGQYLALITLRWPTGQRVVLPRASKRHSTRPSPSEKTNLRNYILQFAGALKLILHPAIDPHLQLSAGSLPIFFMNSPVLKSIYRRTCLTAVTTYWLRSPARLREAACRLATRLPPCQTPFTAYMHSTWCSVTLKVVTLMAFCFCKTSSLRTCSRFNPSSIQTTSCCMPSLPPCQITTGGLNITLCVSKRTQRRQPQTRHHFVAGMGVSSLTVTGFLRPSPTIRQAMSLNTTPRRLQYLWTAVLVSMILSGLKSSWLVRSAPARTVTASQARRSSCPCGKNSGPIMKGRSPECAGTAEPRLRTPLPVASTSVLTTPISTSIVLSSGVATRRVLALVVSVNLPWEKAQVLWMRCNKSRISLRGLSCMWSRVSPLLTQVDTKLAADSPLGVASGETKLTCQTVIMPVPPCSPLVKRSTWSLSPPTCCAAGSSSVPPALGKHTGSSNRSRMVMSFTRQLTRPCLTLGLWGCAGSTSQRVRRCNSLPPLVPARGFASWPAVGVLVRIPFWTKQRIAITLMSGFLAKPPLPAEISNNSTRWVLTLIAMFLTSCLRPNRPSGDSDRISVMPSNQITGTNLCPWSTQPVPRWTNLSGMGKSSPPTTGTERTAPSLSTPVKVPHLMWLHCICPLKIHSTGNEPLLLSPGQDMQSSCMTHTGNCRACLIFLRKAHPSTSQCSVTSSSYIEITKNARLLRLAMEINSGLQTSALILSAPFVQIWKGRAPRSPKLHITWGSISHLIHSLLNSQQNSHPTGPWQPRTMKSGLIGWLPAFAPSINIAARALVQAIWWAPRCFAPQGLCHTTSQNLLGARLKCFLRQSSAPAELRIAGSTSMIGSEKLLSPSHMPSLATSKALPVGDVITSPPDTFRASFLRNQLRSGFLAPEKLQRQFAHQMCTSQILKRTSTQRPSPSAGKCWILEKSDWSGKTRRPIFNLKAAISPGINLQATPHTSEFLLILQCIWTPAWALPFATGGLLGPPIGELTSRSPLMITVPKSFCLVHTMVKCLQGTKFWRARSSRLTTQGTNTLGDLNRIQRICTSLLGMVRTGRIIMKRFGRARKGKFIRLLPPASFIFPRALSLNQLATEMKWGLCRASLTKLVNFLWMLSRNFWCPLLISSYFWPFCLASPSPAGWWSFASDWFAPRYSVRALPFTLSNYRRSYEAFLSQCQVDIPTWGVKHPLGILWHHKVSTLIDEMVSRRMYRIMEKAGQAAWKQVVSEATLSRISNLDVVAHFQHLAAIEAETYKYLASRLPMLHNLRMTGSNVTIVYNSTLNQVFAIFPTSGSRPRLHDSQQWLIAVHSSIFSSVVASCTLFVVLWLRIPMLRSVFGFRWLGAIFLLNSRITRCVRLASPGRPLLRSMNPVGLFGAGGMTDAVRTTMTNGSWFRLASAKATPVFTPGWRSCHSATRPSSIPRYLGGTVKFMLTSRTNSFAPSTTGRTPPCLAMTTFQPYFRPTTNIRSTAVIGFTNGCAPSFPLGWFMFRGFSGVRLQAMFQFKSFRHQDQHYRSIRLCCPPGHQLPVWRLAPSDGSQELSVPHGDRDTRVHHHHSQCHRELFTFFSPHAFLLPFLCFDEKGIQSGIWQCVRHRGCVCLYQLRPTCQGVHPTLLGSRSCATASFHDTDHEVGNRFSLSFCHPTGNLNVQVCWGNAPRAVTRNCFLCGVSCRSVLLCSSTPAATAALIFSFITRYVSMAQIGWQKDLTGQWRLLSFFLCLTLFPMEHSPPAIFLTRLVSLCPPPGSITGGMSVVSMRSVLWLRFASSLGLRRTACPGATLVLDTPTSFWTLRADSIVGGRPLLRKGVRLKSRVTSTSKELCLMVPWQPLPEFQRNNGVVSRRLLPHGSTKGAFGVFHYLYASDDICSKGKSRPTARASAPFDLPELCFYLRVHDIRALSEHKGRAHYGGSSCTSLGGVLSHRNLEIHHLQMPFVLARPQVHSGPCPPRRKCRGLSSDCGKPRICRPASRLHYGRHIGARVEKPRVGWQKSCTGSGKPCQICQITTASSKRERRGTASQSISCARCWVRSSPNKTSPEARDRGRKIIREARRSPIFLRLKKMSGTTSPLVSGNCVCRRSRLPLTRAPGHVPCQIQGGVTLWSLVCRRIILCASASQHHPQHDELAFFGHLGVMIGRMCGEWHLTLCLVTYSIRATVWGSLIGENHAAAIKKKKKKKK'], ['>ORF2_GP2', 'MKWGLCKASLTKLANFLWMLSRSFWCPLLISSYFWPFCLASQSPVGWWSFASDWFAPRYSVRALPFTLSNYRRSYEAFLSQCQVDIPTWGVKHPLGVLWHHKVSTLIDEMVSRRMYRIMEKAGQAAWKQVVSEATLSRISGLDVVAHFQHLAAIEAETCKYLASRLPMLHNLRLTGSNVTIVYNSTLDQVFAIFPTPGSRPKLHDFQQWLIAVHSSIFSSVAASCTLFVVLWLRIPMLRSVFGFRWLGATFLLNSW']]
ex_file = open("newTempFile112233.fasta", "w")
for items in sample_tList:
ex_file.write(items[0] + "\n")
ex_file.write(items[1] + "\n")
ex_file.close()
in_file = '.../msa_example.fasta'
mafft_exe = '/usr/local/bin/mafft'
mafft_cline = MafftCommandline(mafft_exe, input=in_file) #have to change file path
#mafft_cline = MafftCommandline(mafft_exe, input=in_file, localpair=True, lexp=-1.5, lop=0.5)
stdout, stderr = mafft_cline()
print(stdout)
test_align = AlignIO.read(io.StringIO(stdout), "fasta")
#print(test_align)
os.remove("newTempFile112233.fasta")
print('Total time = ' + str(time() - startTime))
startTime = time()
matrix = matlist.blosum62
pWise_align = pairwise2.align.localds(sample_tList[0][1], sample_tList[1][1], matrix, -6, -1)
print(format_alignment(*pWise_align[0]))
print('Total time = ' + str(time() - startTime))
我试图通过参考帮助文档来更改 MAFFT 命令行对齐算法 (http://mafft.cbrc.jp/alignment/software/manual/manual.html). I don't get any error messages, but the alignment output does not change. I'm unsure what adjustments need to be made. I believe that by increasing the gap extension penalty (which is zero by default), the alignment will be improved. I haven't been able to find many documentation examples where custom variables are used when using MAFFT command line on this forum or through Google search. Help is much appreciated. For reference, documentation on the Pairwise2 alignment parameters can be found here: http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html
设法找出可能的解决方案。提供的示例序列的比对导致长 terminal/end 间隙，不应存在。 使用 localpair、lexp 和 lop 更改 MAFFT 对齐算法没有效果（让我很困惑）。然而，当每个输入序列被反转时，我注意到对齐输出的差异。奇怪的是，我能够消除 terminal/end 差距的唯一方法是将 lop（差距开放惩罚）设置为相对于 lexp（差距延伸惩罚）较小的数量。我怀疑我的解决方案是小众的，可能不适用于其他类似的终端间隙。更改对齐设置也可能会降低最佳对齐方式。
展望未来，我计划使用自动化流程 运行 将共有序列与原始序列进行比对。如果我检测到对齐输出不规则（特别是终端间隙），我将尝试反转输入序列并应用自定义对齐设置。我想如果这不是一个一致的解决方案，我会想办法直接改进对齐输出。
对于任何好奇的人，我使用了 -1.5 的 lexp 值和 0.5 的 lop 值（现在包含在我的示例代码的散列行中）。
我一直在尝试使用 MAFFT 命令行工具来识别基因组中的编码区域。我的一般过程是将基因的氨基酸共有序列与目标序列的翻译阅读框进行比对。我的方法在很大程度上是成功的。但是，我注意到一些奇怪的对齐方式，不幸的是它们会妨碍我的注释方法。下面是一个这样的例子（注意——我还包括了来自 Pairwise2 Biopython 模块的成对比对来演示我想要的输出。不幸的是，Pairwise2 的计算时间比 MAFFT 命令行慢了近 20 倍）：
from time import *
from Bio.SubsMat import MatrixInfo as matlist
from Bio import pairwise2
from Bio.pairwise2 import format_alignment
from Bio.Align.Applications import MafftCommandline
startTime = time()
sample_tList = [['>Frame 1', 'RIGVGSIPRHLYCQELPLAQPKTCCAETPFRDSPLQGRLGVCPHLASGVALLYGLSTPLTMSGILDRCTCTPNARVFMAEGQVYCTRCLSARSLLPLNLQVPELGVLGLFYRPEEPLRWTLPRAFPTVECSPAGACWLSAIFPIARMTSGNLNFQQRMVRVAAEIYRAGQLTPAVLKVLQVYERGCRWYPIVGPVPGVGVYANSLHVSDKPFPGATHVLTNLPLPQRPKPEDFCPFECAMADVYDIGHGAVMFVAGGKVSWAPRGGDEVRFETVPEELKLIANRLHISFPPHHLVDMSKFAFIVPGSGVSLRVEHQHGCLPADIVPKGNCWWCLFDLLPPGVQNREIRYANQFGYQTKHGVSGKYLQRRLQINGLRAVTDTHGPIVVQYFSVKESWIRHFRLAGEPSLPGFEDLLRIRVESNTSPLADKDEKIFRFGSHKWYGAGKRARKARSGATTTVAHRASSARETRQAKKHEGVDANNAAHLEHYSPPAEGNCGWHCISAIVNRMVNSNFETTLPERVRPSDDWATDEDFVNTIQILRLPAALDRNGACKSAKYVLKLEGEHWTVSVAPGMSPSLLPLECVQGCCEHKGGLGSPDAVEVSGFDPTCLDRLAEVMHLPSSVIPAALAEMSNNSDRPASLVNTAWTVSQFYARHTGGNHRDQVRLGKIISLCQVIEECCCHQNKTNRATPEEVAAKIDQYLRGATSLEECLIKLERVSPPSAADTSFDWNVVLPGVEAAGPTTEQPHANQCCAPVPVVTQEPLDKDSVPLTAFSLSNCYYPAQGDEVRHRERLNSVLSKLEEVVLEEYGLMPTGLGPRPVLPSGLDELKDQMEEDLLKLANAQATSEMMALAAEQVDLKAWVKSYPRWIPPPPPPKVQPRRMKPVKSLPENKPVPAPRRKVRSDPGKSILAVGGPLNFSTPSELVTPLGEPVLMPASQHVSRPVTPLSEPAPVPAPRRIVSRPMTPLSEPTFVFAPWRKSQQVEEANPAAATLTCQDEPLDLSASSQTEYEAYPLAPLENIGVLEAGGQEAEEVLSGISDILDNTNPAPVSSSSSLSSVKITRPKYSAQAIIDSGGPCSGHLQKEKEACLRIMREACDAARLGDPATQEWLSHMWDRVDVLTWRNTSVYQAFRTLDGRFGFLPKMILETPPPYPCGFVMLPHTPTPSVSAESDLTIGSVATEDVPRILGKTENTGNVLNQKPLALFEEEPVCDQPAKDSRTLSRESGDSTTAPPVGTGGAGLPTDLPPLDGVDADGGGLLRTAKGKAERFFDQLSRQVFNIVSHLPVFFSHLFKSDSGYSPGDWGFAAFTLFCLFLCYSYPFFGFAPLLGVFSGSSRRVRMGVFGCWLAFAVGLFKPVSDPVGAACEFDSPECRNILHSFELLKPWDPVRSLVVGPVGLGLAILGRLLGGARYIWHFLLRLGIVADCILAGAYVLSQGRCKKCWGSCIRTAPNEIAFNVFPFTRATRSSLIDLCDRFCAPKGMDPIFLATGWRGCWTGQSPIEQPSEKPIAFAQLDEKRITARTVVSQPYDPNQAVKCLRVLQAGGAMVAEAVPKVVKVSAIPFRAPFFPTGVKVDPECRIVVDPDTFTTALRSGYSTTNLVLGVGDFAQLNGLKIRQISKPSGGGPHLIAALHVACSMVLHMLAGVYVTAVGSCGTGTSDPWCANPFAVPGYGPGSLCTSRLCISQHGLTLPLTALVAGFGLQEIALVVLIFVSIGGMAHRLSCKADMLCILLAIASYVWVPLTWLLCVFPCWLRWFSLHPLTILWLVFFLISVNMPSGILAVVLLVSLWLLGRYTNIAGLVTPYDIHHYTSGPRGVAALATAPDGTYLAAVRRAALTGRTMLFTPSQLGSLLEGAFRTRKPSLNTVNVVGSSMGSGGVFTIDGRIKCVTAAHVLTGNSARVSGVGFNQMLDFDVKGDFAIADCPNWQGVAPKTQFCGDGWTGRAYWLTSSGVEPGVIGDGFAFCFTACGDSGSPVITEAGELVGVHTGSNKQGGGIVTRPSGQFCNVTPIKLSELSEFFAGPKVPLGDVKVGSHIIKDTSEVPSDLCALLAAKPELEGGLSTVQLLCVFFLLWRMMGHAWTPLVAVGFFILNEVLPAVLVRSVFSFGMFALSWLTPWSAQVLMIRLLTAALNRNRVSLIFYSLGAVTGFVADLATTQGHPLQAVMNLSTYAFLPRMMVVTSPVPAIACGVVHLLAIILYLFKYRCLHHVLVGDGAFSAAFFLRYFAEGKLREGVSQSCGMSHESLTGALAIKLSDEDLDFLTKWTDFKCFVSASNMRNAAGQFIEAAYAKALRIELAQLVQVDKVRGTLAKLEAFADTVAPQLSPGDIVVALGHTPVGSIFDLKVGSTKHTLQAIETRVLAGSKMTVARVVDPTPAPPPAPVPIPLPPKVLENGPNAWGGEDRLNKRKRRRMEAVGIFVMDGKKYQKFWDKNSGDVFYEEVHNSTDEWECLRAGDPADFDPETGIQCGHVTIEDKVYNVFTSPSGRRFLVPANPENRRIQWEAARLSVEQALGMMNVDGELTAKELEKLKRIIDKLQGLTKEQCLNCPPVAPAVVAAAWLLLRQRKNFTTGPSPDLTKWPVRLSRTRSSTTNIRLPNRLMVVLCSCAPLFLRLMSSPALMHLLSYLPATGRETLGLMARFGILRPRPPKRKSHLVRKYRLVTLGAVTHLKLVSLISCTLLGATLSGKEFYRIQGLETYLTEPPVTLEAQCMRLPASRPMLLRLMGVPSWPQPCPPVLSCMYRPFQRPSLIILILGLTALNSQSTVVRMLLGTSPNTICPPKALFCLEFFALCGSTCLPMWVSARPFIGLPLTLPRILWLEMGTDFQPRIFRASLKSTFCAHRLCEKTGKLLLLVPSRSSIVGRRRLGQYLALITLRWPTGQRVVLPRASKRHSTRPSPSEKTNLRNYILQFAGALKLILHPAIDPHLQLSAGSLPIFFMNSPVLKSIYRRTCLTAVTTYWLRSPARLREAACRLATRLPPCQTPFTAYMHSTWCSVTLKVVTLMAFCFCKTSSLRTCSRFNPSSIQTTSCCMPSLPPCQITTGGLNITLCVSKRTQRRQPQTRHHFVAGMGVSSLTVTGFLRPSPTIRQAMSLNTTPRRLQYLWTAVLVSMILSGLKSSWLVRSAPARTVTASQARRSSCPCGKNSGPIMKGRSPECAGTAEPRLRTPLPVASTSVLTTPISTSIVLSSGVATRRVLALVVSVNLPWEKAQVLWMRCNKSRISLRGLSCMWSRVSPLLTQVDTKLAADSPLGVASGETKLTCQTVIMPVPPCSPLVKRSTWSLSPPTCCAAGSSSVPPALGKHTGSSNRSRMVMSFTRQLTRPCLTLGLWGCAGSTSQRVRRCNSLPPLVPARGFASWPAVGVLVRIPFWTKQRIAITLMSGFLAKPPLPAEISNNSTRWVLTLIAMFLTSCLRPNRPSGDSDRISVMPSNQITGTNLCPWSTQPVPRWTNLSGMGKSSPPTTGTERTAPSLSTPVKVPHLMWLHCICPLKIHSTGNEPLLLSPGQDMQSSCMTHTGNCRACLIFLRKAHPSTSQCSVTSSSYIEITKNARLLRLAMEINSGLQTSALILSAPFVQIWKGRAPRSPKLHITWGSISHLIHSLLNSQQNSHPTGPWQPRTMKSGLIGWLPAFAPSINIAARALVQAIWWAPRCFAPQGLCHTTSQNLLGARLKCFLRQSSAPAELRIAGSTSMIGSEKLLSPSHMPSLATSKALPVGDVITSPPDTFRASFLRNQLRSGFLAPEKLQRQFAHQMCTSQILKRTSTQRPSPSAGKCWILEKSDWSGKTRRPIFNLKAAISPGINLQATPHTSEFLLILQCIWTPAWALPFATGGLLGPPIGELTSRSPLMITVPKSFCLVHTMVKCLQGTKFWRARSSRLTTQGTNTLGDLNRIQRICTSLLGMVRTGRIIMKRFGRARKGKFIRLLPPASFIFPRALSLNQLATEMKWGLCRASLTKLVNFLWMLSRNFWCPLLISSYFWPFCLASPSPAGWWSFASDWFAPRYSVRALPFTLSNYRRSYEAFLSQCQVDIPTWGVKHPLGILWHHKVSTLIDEMVSRRMYRIMEKAGQAAWKQVVSEATLSRISNLDVVAHFQHLAAIEAETYKYLASRLPMLHNLRMTGSNVTIVYNSTLNQVFAIFPTSGSRPRLHDSQQWLIAVHSSIFSSVVASCTLFVVLWLRIPMLRSVFGFRWLGAIFLLNSRITRCVRLASPGRPLLRSMNPVGLFGAGGMTDAVRTTMTNGSWFRLASAKATPVFTPGWRSCHSATRPSSIPRYLGGTVKFMLTSRTNSFAPSTTGRTPPCLAMTTFQPYFRPTTNIRSTAVIGFTNGCAPSFPLGWFMFRGFSGVRLQAMFQFKSFRHQDQHYRSIRLCCPPGHQLPVWRLAPSDGSQELSVPHGDRDTRVHHHHSQCHRELFTFFSPHAFLLPFLCFDEKGIQSGIWQCVRHRGCVCLYQLRPTCQGVHPTLLGSRSCATASFHDTDHEVGNRFSLSFCHPTGNLNVQVCWGNAPRAVTRNCFLCGVSCRSVLLCSSTPAATAALIFSFITRYVSMAQIGWQKDLTGQWRLLSFFLCLTLFPMEHSPPAIFLTRLVSLCPPPGSITGGMSVVSMRSVLWLRFASSLGLRRTACPGATLVLDTPTSFWTLRADSIVGGRPLLRKGVRLKSRVTSTSKELCLMVPWQPLPEFQRNNGVVSRRLLPHGSTKGAFGVFHYLYASDDICSKGKSRPTARASAPFDLPELCFYLRVHDIRALSEHKGRAHYGGSSCTSLGGVLSHRNLEIHHLQMPFVLARPQVHSGPCPPRRKCRGLSSDCGKPRICRPASRLHYGRHIGARVEKPRVGWQKSCTGSGKPCQICQITTASSKRERRGTASQSISCARCWVRSSPNKTSPEARDRGRKIIREARRSPIFLRLKKMSGTTSPLVSGNCVCRRSRLPLTRAPGHVPCQIQGGVTLWSLVCRRIILCASASQHHPQHDELAFFGHLGVMIGRMCGEWHLTLCLVTYSIRATVWGSLIGENHAAAIKKKKKKKK'], ['>ORF2_GP2', 'MKWGLCKASLTKLANFLWMLSRSFWCPLLISSYFWPFCLASQSPVGWWSFASDWFAPRYSVRALPFTLSNYRRSYEAFLSQCQVDIPTWGVKHPLGVLWHHKVSTLIDEMVSRRMYRIMEKAGQAAWKQVVSEATLSRISGLDVVAHFQHLAAIEAETCKYLASRLPMLHNLRLTGSNVTIVYNSTLDQVFAIFPTPGSRPKLHDFQQWLIAVHSSIFSSVAASCTLFVVLWLRIPMLRSVFGFRWLGATFLLNSW']]
ex_file = open("newTempFile112233.fasta", "w")
for items in sample_tList:
ex_file.write(items[0] + "\n")
ex_file.write(items[1] + "\n")
ex_file.close()
in_file = '.../msa_example.fasta'
mafft_exe = '/usr/local/bin/mafft'
mafft_cline = MafftCommandline(mafft_exe, input=in_file) #have to change file path
#mafft_cline = MafftCommandline(mafft_exe, input=in_file, localpair=True, lexp=-1.5, lop=0.5)
stdout, stderr = mafft_cline()
print(stdout)
test_align = AlignIO.read(io.StringIO(stdout), "fasta")
#print(test_align)
os.remove("newTempFile112233.fasta")
print('Total time = ' + str(time() - startTime))
startTime = time()
matrix = matlist.blosum62
pWise_align = pairwise2.align.localds(sample_tList[0][1], sample_tList[1][1], matrix, -6, -1)
print(format_alignment(*pWise_align[0]))
print('Total time = ' + str(time() - startTime))
我试图通过参考帮助文档来更改 MAFFT 命令行对齐算法 (http://mafft.cbrc.jp/alignment/software/manual/manual.html). I don't get any error messages, but the alignment output does not change. I'm unsure what adjustments need to be made. I believe that by increasing the gap extension penalty (which is zero by default), the alignment will be improved. I haven't been able to find many documentation examples where custom variables are used when using MAFFT command line on this forum or through Google search. Help is much appreciated. For reference, documentation on the Pairwise2 alignment parameters can be found here: http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html
设法找出可能的解决方案。提供的示例序列的比对导致长 terminal/end 间隙，不应存在。 使用 localpair、lexp 和 lop 更改 MAFFT 对齐算法没有效果（让我很困惑）。然而，当每个输入序列被反转时，我注意到对齐输出的差异。奇怪的是，我能够消除 terminal/end 差距的唯一方法是将 lop（差距开放惩罚）设置为相对于 lexp（差距延伸惩罚）较小的数量。我怀疑我的解决方案是小众的，可能不适用于其他类似的终端间隙。更改对齐设置也可能会降低最佳对齐方式。
展望未来，我计划使用自动化流程 运行 将共有序列与原始序列进行比对。如果我检测到对齐输出不规则（特别是终端间隙），我将尝试反转输入序列并应用自定义对齐设置。我想如果这不是一个一致的解决方案，我会想办法直接改进对齐输出。
对于任何好奇的人，我使用了 -1.5 的 lexp 值和 0.5 的 lop 值（现在包含在我的示例代码的散列行中）。