pairwise2 module and globalds
0
0
Entering edit mode
18 months ago

hello everyone, my question is, after applying pairwise2 , how do i extract score from globalds without using pairwise aligner and using the 'count' variable or defining a function. i want them in a row so that i can calculate the similarity thanks a lott in advance

alignments_fish_human = pairwise2.align.globalds(fish.seq,human.seq,blosum62,-5,-0.5) alignments_fish_squirrel = pairwise2.align.globalds(fish.seq, squirrel.seq,blosum62,-5,-0.5) alignments_fish_rat = pairwise2.align.globalds(fish.seq,rat.seq,blosum62,-5,-0.5) alignments_human_squirrel = pairwise2.align.globalds(human.seq,squirrel.seq,blosum62,-5,-0.5) alignments_human_rat = pairwise2.align.globalds(human.seq,rat.seq,blosum62,-5,-0.5) alignments_squirrel_rat = pairwise2.align.globalds(squirrel.seq,rat.seq,blosum62,-5,-0.5)

print(pairwise2.format_alignment(alignments_fish_human[0])) print(pairwise2.format_alignment(alignments_fish_squirrel[0])) print(pairwise2.format_alignment(alignments_fish_rat[0])) print(pairwise2.format_alignment(alignments_human_squirrel[0])) print(pairwise2.format_alignment(alignments_human_rat[0])) print(pairwise2.format_alignment(alignments_squirrel_rat[0]))

MSNT-VYISVLVVVLATGCLS----KPLSG-PHNNGGIVLERTGKYPSGNGAG------WLARRAAPLRAEELISKLLPQIQEAG---LLNQAD--RYQ---LRDVLHQMHDRDYTGWMDFGRRSIEEYELDS |... || ||...||....| ||.|. | ..|.|.||. ||... .| |......|.|| | |. || ..| |.. ....| |||||||||.|. .. MQRLCVY--VLIFALALAAFSEASWKPRSQQP------------DAPLGTGANRDLELPWLEQQ-GP--ASHHRRQLGPQ----GPPHLV--ADPSKKQGPWLEE-----EEEAY-GWMDFGRRSAED---EN Score=110

MSNT-VYISVLVVVLATGCLSK------------PLSGPHNNGGIVLERTGKYPSGNGAGWLAR-----RAAP-LRAEELISKLL-PQIQEAGLLNQADRYQLRDVLHQMHDRDYTGWMDFGRRSIEEYELDS |... || .||.|||....|. || ||..|.| || |. ||.| |..| |.|. .||.. |...| ..| .| |||||||||.||..... MQRLCVY--ALVLVLALAAFSEASWKSRSQLQDAPL-GPVTNKG--LE-----PQ-----WLDRRQLGPRGPPHLVAD--LSKKQGPWMEE----EEA-AY---------------GWMDFGRRSAEEGDQXP Score=121.5

and so on

sequence alignment • 588 views
ADD COMMENT

Login before adding your answer.

Traffic: 2874 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6