Hi,
This is the align_multiple.ali file of automodel example,
C; A multiple alignment in the PIR format; used in tutorial
>P1;5fd1 structureX:5fd1:1 :A:106 :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*
>P1;1bqx structureN:1bqx: 1 :A: 77 :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00 AYVITEPCIGTKCASCVEVCPVDCIHEGEDQYYIDPDVCIDCGACEAVCPVSAIYHEDFVPEEWKSYIQKNRDFF KK-----------------------------*
>P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00 AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED----------------- -------------------------------*
modelmultilple.py has this code;
a = automodel(env, alnfile = 'align-multiple.ali', # alignment filename knowns = ('5fd1', '1bqx'), # codes of the templates sequence = '1fdx') # code of the target
I dont understand this. I mean the real purpose of this code. I thought 'sequence' is the target we want to achieve and it has no gaps. but here 1fdx has so many breaks. Could anyone tell me the real meaning of this alignment.
Thanking you