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*

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Sincerely, Kim