The LocalAlignBestPam Function

The function LocalAlignBestPam alternates between two different optimizations. Given a Match structure, it will call LocalAlign (to improve the local alignment) followed by a call to FindBestPam (to find the best PAM distance) until the similarity score no longer increases.

> DB := ReadDb('~cbrg/DB/SwissProt'):
> CreateDayMatrices():
> m := Match(op(Sequence(Entry(8588))), op(Sequence(Entry(8577)))):
> m := LocalAlignBestPam(m, DMS);
> print(m);
lengths=97,110 simil=275.3, PAM_dist=85.9883, offsets=5978923,5974267,
  identity=40.4%, similarity=12.3%
ID=CY2_RHOVI   AC=P00083;   DE=CYTOCHROME C2 PRECURSOR.   OS=RHODOPSEUDOMONAS
VIRIDIS.   RES=1.6   
ID=CY22_RHOPA   AC=P00091;   DE=CYTOCHROME C2.   OS=RHODOPSEUDOMONAS PALUSTRIS
(STRAIN ATCC 17007 / 2.1.37).   
  hhhhhhhthhhhtt    tt         tt     tt        hhhht         hhhhhhhhh hhh     
QDAASGEQVFKQCLVCHSIGPGAKNKVGPVLNGLFGRHSGTIEGFAYSDANKNS___GITWTEEVFREYIRDPKA_____
|||.:||.|||||!.||.   ..||.|||.|.|:.||.:||..||.||..|.||   |:.||.! . .|:.||.|     
QDAKAGEAVFKQCMTCHR___ADKNMVGPALGGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIINYLNDPNAFLKKF

         t tt          hhhhhhhhhh 
_________KIPGTKMIFAGVKDEQKVSDLIAYI
         .!. |||.|. :.:||:..|:!||:
LTDKGKADQAVGVTKMTFK_LANEQQRKDVVAYL

The results of a LocalAlignBestPam should be compared with a call to LocalAlign. Recall LocalAlign aligns at one particular PAM distance. Here we calculate it at PAM 250.

> ref := LocalAlign(m, DM);
ref := Match(166.1,5978923,5974267,72,72,250,171.449)
> print(ref);
lengths=72,72 simil=166.1, PAM_dist=250, offsets=5978923,5974267,
  identity=49.3%, similarity=26.7%
ID=CY2_RHOVI   AC=P00083;   DE=CYTOCHROME C2 PRECURSOR.   OS=RHODOPSEUDOMONAS
VIRIDIS.   RES=1.6   
ID=CY22_RHOPA   AC=P00091;   DE=CYTOCHROME C2.   OS=RHODOPSEUDOMONAS PALUSTRIS
(STRAIN ATCC 17007 / 2.1.37).   
  hhhhhhhthhhhtt    tt         tt     tt        hhhht         hhhhhhhhh hhh
QDAASGEQVFKQCLVCHSIGPGAKNKVGPVLNGLFGRHSGTIEGFAYSDANKNSG___ITWTEEVFREYIRDPKA
|||.:||.|||||!:||.   :.||.|||:|:|::||::||..||:||..|:|||   !:||.!.:.:|!:||:|
QDAKAGEAVFKQCMTCHR___ADKNMVGPALGGVVGRKAGTAAGFTYSPLNHNSGEAGLVWTADNIINYLNDPNA

The similarity score is well over one hundred points lower and the alignment is approximately thirty bases shorter.

Whenever the user would like to obtain the best alignment possible between two sequences, the LocalAlignBestPam function should be used.