Merge twp alignment files - modeller_usage

26 Oct 2004


      Hi, all
I made two alignment files with a threading program other than MODELLER.
How can I merge these two alignment files?
Each alignment file containts one query sequence and one template sequence.
Query sequences from two alignment files are same to each  other  and  have different gaps.
Following sequences and gaps are made randomly.
file1: 1aaab.ali
>P1;source
sequence: query : 1: : 700: : target sequence:  unknown: : 
MASNMLDS--------KFLDKLDFJLSDKFLKDFLSJFDLJFLKDJFLDKFLS*
>P1;1aaab
structure: 1aaab: 100: B : 800: B: template: known structure: :
M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD--------*
file2: 1bbbc.ali
>P1;source
sequence: query : 1: : 700: : target sequence:  unknown: : 
MASNMLDSKFLDKLDFJLSDKFLKD----------FLSJFDLJFLKDJFLDKFLS*
>P1;1bbbc
structure: 1bbbc : 40: C : 700: C : template: known structure: :
M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD----------*
******MY TARGET ALIGNMENT FORM*********************
>P1;source
sequence: query : 1: : 700: : target sequence:  unknown: : 
MASNMLDSKF---LDKLDFJLSDKFLKD--FLSJFDLJFLKDJFLDKFLS*
>P1;1aaab
structure: 1aaab: 100: B : 800: B: template: known structure: :
M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD-----*
>P1;1bbbc
structure: 1bbbc : 40: C : 700: C : template: known structure: :
M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDS-----AD*
******************************************************
Sincerely,
Kim