Module xi_covutils.matrices.blosum_80

Background and joint amino acid substitution frequencies used to calculate BLOSUM80 matrix.

Frequencies taken from the NCBI C++ toolkit source code. https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/algo/blast/composition_adjustment/matrix_frequency_data.c

Expand source code
"""
Background and joint amino acid substitution frequencies used to calculate
BLOSUM80 matrix.

Frequencies taken from the NCBI C++ toolkit source code.
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/algo/blast/composition_adjustment/matrix_frequency_data.c

"""
BLOSUM_80_BG = [
  7.2647227078731003e-02, 5.0418078079712533e-02, 4.2998652475215837e-02,
  5.3630877849155469e-02, 2.8859643195758448e-02, 3.3634522394591609e-02,
  5.4557686298480158e-02, 7.6673641116832586e-02, 2.5417438256716121e-02,
  6.7169462169032662e-02, 9.9526086073919384e-02, 5.4794439692059750e-02,
  2.4441485110408976e-02, 4.7108293477054419e-02, 3.8215524905474578e-02,
  5.7239465972425123e-02, 5.0130851564694504e-02, 1.4489654685450317e-02,
  3.4849727270340386e-02, 7.3197242333946158e-02
]

BLOSUM_80_JOINT = [
  [
    2.5190801261944146e-02, 2.0340063576029794e-03, 1.5934450456787860e-03,
    1.7567882204091898e-03, 1.5342531535382758e-03, 1.7000666571091031e-03,
    2.7868757423594017e-03, 5.3312141672192219e-03, 9.4989551434358397e-04,
    2.6511420856442343e-03, 3.6482390472164553e-03, 2.8776040054767438e-03,
    1.1106592033970583e-03, 1.3579821676123010e-03, 2.1407549535065536e-03,
    6.3814552201747433e-03, 3.5676984041129148e-03, 3.2555946863964375e-04,
    1.1044305938818220e-03, 4.6043558088638440e-03
  ],
  [
    2.0340063576029794e-03, 2.0957619284835711e-02, 1.6758487367421928e-03,
    1.2888167784480715e-03, 3.3826512646630144e-04, 2.3643445818728338e-03,
    2.2882006533010476e-03, 1.4590947777562337e-03, 1.1860735000568496e-03,
    1.0137588625981279e-03, 1.8206526954490602e-03, 6.0560763047425702e-03,
    6.2337540140620625e-04, 6.8229547250252861e-04, 8.5854176274829876e-04,
    2.0042877649097124e-03, 1.5124193439838248e-03, 2.1495826193954981e-04,
    7.3405490506437917e-04, 1.3053875072860433e-03
  ],
  [
    1.5934450456787860e-03, 1.6758487367421928e-03, 1.6571102507116985e-02,
    3.6538256029687933e-03, 3.7275314562150083e-04, 1.3857458787672526e-03,
    1.9028611939066358e-03, 2.5087252791082940e-03, 1.2287120285654496e-03,
    7.4457563298143141e-04, 1.0685540535108611e-03, 2.2109484306704398e-03,
    4.0104114114639772e-04, 5.5233725060967317e-04, 6.5378230775305264e-04,
    2.8681766931253736e-03, 1.9573168921473445e-03, 1.3788261408849363e-04,
    5.7618561566013431e-04, 9.3483242504674316e-04
  ],
  [
    1.7567882204091898e-03, 1.2888167784480715e-03, 3.6538256029687933e-03,
    2.6192308612565114e-02, 3.3106691118318270e-04, 1.3768335120404338e-03,
    4.7855109048933571e-03, 2.2232114513351937e-03, 8.1024112807968755e-04,
    7.7107432004201270e-04, 1.0524113745173926e-03, 1.9891158615195038e-03,
    3.3025592590943029e-04, 5.9228818844263222e-04, 9.2722402594094192e-04,
    2.3761553355682980e-03, 1.6423964465390574e-03, 1.1250313032631603e-04,
    4.5827153005301055e-04, 9.6057858837385150e-04
  ],
  [
    1.5342531535382758e-03, 3.3826512646630144e-04, 3.7275314562150083e-04,
    3.3106691118318270e-04, 1.7242275829262476e-02, 2.8646474074708189e-04,
    2.8282275916935814e-04, 6.0199758435290119e-04, 1.6234838273827443e-04,
    1.1265997431595498e-03, 1.4150540356314203e-03, 3.8133934535800398e-04,
    3.5227309589971249e-04, 5.3668272671786679e-04, 2.9686417147468063e-04,
    9.5169015207393563e-04, 8.7056289887733830e-04, 1.2638354788184329e-04,
    3.0970164723884082e-04, 1.3402441983659027e-03
  ],
  [
    1.7000666571091031e-03, 2.3643445818728338e-03, 1.3857458787672526e-03,
    1.3768335120404338e-03, 2.8646474074708189e-04, 9.4347765835274943e-03,
    3.4983547675341785e-03, 1.0949548858705770e-03, 1.1246735029182945e-03,
    6.9825772263661188e-04, 1.3621164757556699e-03, 2.8087671852638188e-03,
    7.2881923779495811e-04, 4.5182331847654853e-04, 6.9151715980429068e-04,
    1.6537440549432947e-03, 1.2213788117405877e-03, 1.9879174677422644e-04,
    5.4136767114461271e-04, 1.0117238998697397e-03
  ],
  [
    2.7868757423594017e-03, 2.2882006533010476e-03, 1.9028611939066358e-03,
    4.7855109048933571e-03, 2.8282275916935814e-04, 3.4983547675341785e-03,
    2.0820161672110919e-02, 1.6705768658803739e-03, 1.2497919872780897e-03,
    9.6840513155216357e-04, 1.4960914225340589e-03, 3.5721908719380593e-03,
    5.7149419172049785e-04, 6.3988473796368903e-04, 1.2122196186289647e-03,
    2.6389347134212079e-03, 1.8749387967046983e-03, 1.9036380224872525e-04,
    6.3290036404780182e-04, 1.4751061012869160e-03
  ],
  [
    5.3312141672192219e-03, 1.4590947777562337e-03, 2.5087252791082940e-03,
    2.2232114513351937e-03, 6.0199758435290119e-04, 1.0949548858705770e-03,
    1.6705768658803739e-03, 4.6339669111671353e-02, 7.5449961042330647e-04,
    9.4996724611759150e-04, 1.6066592192185663e-03, 2.0310505314366269e-03,
    5.3609624387219209e-04, 8.9864424405597940e-04, 1.0176342727297918e-03,
    3.4421697217907042e-03, 1.8920241991862482e-03, 2.9373791998702517e-04,
    6.1327956332154923e-04, 1.4084342214988788e-03
  ],
  [
    9.4989551434358397e-04, 1.1860735000568496e-03, 1.2287120285654496e-03,
    8.1024112807968755e-04, 1.6234838273827443e-04, 1.1246735029182945e-03,
    1.2497919872780897e-03, 7.5449961042330647e-04, 1.0381617825381334e-02,
    4.4036371570812095e-04, 7.9508382719793930e-04, 1.0307766502203480e-03,
    2.6842308809614442e-04, 6.8472295590456679e-04, 4.0762982846324675e-04,
    9.6226821486916257e-04, 6.8751986685796880e-04, 1.4371608217276840e-04,
    1.6115232208711219e-03, 5.3755732656986873e-04
  ],
  [
    2.6511420856442343e-03, 1.0137588625981279e-03, 7.4457563298143141e-04,
    7.7107432004201270e-04, 1.1265997431595498e-03, 6.9825772263661188e-04,
    9.6840513155216357e-04, 9.4996724611759150e-04, 4.4036371570812095e-04,
    2.1961426293375986e-02, 1.1130703369690390e-02, 1.1532712305851239e-03,
    2.4830606782385335e-03, 2.6597759616518901e-03, 7.3360010098323712e-04,
    1.4571406164888326e-03, 2.3588073239766052e-03, 3.3397592349852914e-04,
    1.2624333898651637e-03, 1.2271122820238527e-02
  ],
  [
    3.6482390472164553e-03, 1.8206526954490602e-03, 1.0685540535108611e-03,
    1.0524113745173926e-03, 1.4150540356314203e-03, 1.3621164757556699e-03,
    1.4960914225340589e-03, 1.6066592192185663e-03, 7.9508382719793930e-04,
    1.1130703369690390e-02, 4.4208543625750947e-02, 1.9460828295282577e-03,
    5.1637253946183711e-03, 5.2243696624605148e-03, 1.1528201208432873e-03,
    2.0991567569779157e-03, 2.7981964830167271e-03, 6.3277768036502599e-04,
    2.0134515231625665e-03, 8.8913964764739482e-03
  ],
  [
    2.8776040054767438e-03, 6.0560763047425702e-03, 2.2109484306704398e-03,
    1.9891158615195038e-03, 3.8133934535800398e-04, 2.8087671852638188e-03,
    3.5721908719380593e-03, 2.0310505314366269e-03, 1.0307766502203480e-03,
    1.1532712305851239e-03, 1.9460828295282577e-03, 1.8992311051287718e-02,
    7.1570376147636942e-04, 7.2977429729635017e-04, 1.2494764855845110e-03,
    2.5724600423967150e-03, 2.0209702186968510e-03, 1.9168209136920497e-04,
    7.8006357431686252e-04, 1.4847749228956784e-03
  ],
  [
    1.1106592033970583e-03, 6.2337540140620625e-04, 4.0104114114639772e-04,
    3.3025592590943029e-04, 3.5227309589971249e-04, 7.2881923779495811e-04,
    5.7149419172049785e-04, 5.3609624387219209e-04, 2.6842308809614442e-04,
    2.4830606782385335e-03, 5.1637253946183711e-03, 7.1570376147636942e-04,
    5.3068580972096564e-03, 1.0285774291964053e-03, 3.3805426284931307e-04,
    6.9732452132326552e-04, 9.2870717652810894e-04, 1.9855470215781828e-04,
    4.6842552580683944e-04, 2.1900560317616967e-03
  ],
  [
    1.3579821676123010e-03, 6.8229547250252861e-04, 5.5233725060967317e-04,
    5.9228818844263222e-04, 5.3668272671786679e-04, 4.5182331847654853e-04,
    6.3988473796368903e-04, 8.9864424405597940e-04, 6.8472295590456679e-04,
    2.6597759616518901e-03, 5.2243696624605148e-03, 7.2977429729635017e-04,
    1.0285774291964053e-03, 2.1050081047094053e-02, 4.2695305789420819e-04,
    9.9526342159352650e-04, 1.0513746746114907e-03, 7.4360162788489814e-04,
    4.5643669065202081e-03, 2.2374943285650862e-03
  ],
  [
    2.1407549535065536e-03, 8.5854176274829876e-04, 6.5378230775305264e-04,
    9.2722402594094192e-04, 2.9686417147468063e-04, 6.9151715980429068e-04,
    1.2122196186289647e-03, 1.0176342727297918e-03, 4.0762982846324675e-04,
    7.3360010098323712e-04, 1.1528201208432873e-03, 1.2494764855845110e-03,
    3.3805426284931307e-04, 4.2695305789420819e-04, 2.2132147568842062e-02,
    1.4255613382498733e-03, 1.0735194808918437e-03, 9.8582208625861730e-05,
    3.4299989987846913e-04, 1.0356422797820938e-03
  ],
  [
    6.3814552201747433e-03, 2.0042877649097124e-03, 2.8681766931253736e-03,
    2.3761553355682980e-03, 9.5169015207393563e-04, 1.6537440549432947e-03,
    2.6389347134212079e-03, 3.4421697217907042e-03, 9.6226821486916257e-04,
    1.4571406164888326e-03, 2.0991567569779157e-03, 2.5724600423967150e-03,
    6.9732452132326552e-04, 9.9526342159352650e-04, 1.4255613382498733e-03,
    1.6728326838562371e-02, 4.7707748874885403e-03, 2.2457429196472549e-04,
    9.2159836957901727e-04, 2.0684030169239110e-03
  ],
  [
    3.5676984041129148e-03, 1.5124193439838248e-03, 1.9573168921473445e-03,
    1.6423964465390574e-03, 8.7056289887733830e-04, 1.2213788117405877e-03,
    1.8749387967046983e-03, 1.8920241991862482e-03, 6.8751986685796880e-04,
    2.3588073239766052e-03, 2.7981964830167271e-03, 2.0209702186968510e-03,
    9.2870717652810894e-04, 1.0513746746114907e-03, 1.0735194808918437e-03,
    4.7707748874885403e-03, 1.5594999664688735e-02, 2.0707952088013908e-04,
    8.2888908190237710e-04, 3.2712773918631040e-03
  ],
  [
    3.2555946863964375e-04, 2.1495826193954981e-04, 1.3788261408849363e-04,
    1.1250313032631603e-04, 1.2638354788184329e-04, 1.9879174677422644e-04,
    1.9036380224872525e-04, 2.9373791998702517e-04, 1.4371608217276840e-04,
    3.3397592349852914e-04, 6.3277768036502599e-04, 1.9168209136920497e-04,
    1.9855470215781828e-04, 7.4360162788489814e-04, 9.8582208625861730e-05,
    2.2457429196472549e-04, 2.0707952088013908e-04, 8.7238920952867408e-03,
    1.0281252180987448e-03, 3.6291275126003661e-04
  ],
  [
    1.1044305938818220e-03, 7.3405490506437917e-04, 5.7618561566013431e-04,
    4.5827153005301055e-04, 3.0970164723884082e-04, 5.4136767114461271e-04,
    6.3290036404780182e-04, 6.1327956332154923e-04, 1.6115232208711219e-03,
    1.2624333898651637e-03, 2.0134515231625665e-03, 7.8006357431686252e-04,
    4.6842552580683944e-04, 4.5643669065202081e-03, 3.4299989987846913e-04,
    9.2159836957901727e-04, 8.2888908190237710e-04, 1.0281252180987448e-03,
    1.4809695895202394e-02, 1.2479627747244684e-03
  ],
  [
    4.6043558088638440e-03, 1.3053875072860433e-03, 9.3483242504674316e-04,
    9.6057858837385150e-04, 1.3402441983659027e-03, 1.0117238998697397e-03,
    1.4751061012869160e-03, 1.4084342214988788e-03, 5.3755732656986873e-04,
    1.2271122820238527e-02, 8.8913964764739482e-03, 1.4847749228956784e-03,
    2.1900560317616967e-03, 2.2374943285650862e-03, 1.0356422797820938e-03,
    2.0684030169239110e-03, 3.2712773918631040e-03, 3.6291275126003661e-04,
    1.2479627747244684e-03, 2.4557979462295820e-02
  ]
]