[BioPython] Clustalw pair wise alignment

[Stefanie Lück]

Hi!

 

I working with clustalw and everything works fine. No I have some questions:

 

1) Must the input data be in a file or can it also be in the code (e.g. in a list)?

 

2) Because, I want to do many (up to hundreds) pair wise alignments (short sequences) and I don't want to store each of them in a separate file. 

If I have it in one file, clustalw make a multiple alignment:

 

Match1                              ------CAAGATTTGAGCACCACAGGCAA---
full1                                  ------CAAGATTTGAGCACCACAGGCAACAG
Match0                              AGCCTTCAAGATTTGAGCACCACAG-------
full0                                   AGCCTTCAAGATTTGAGCACCACAG-------

 

whereas Match1 should only align to full1 and so on.

 

Could someone give a hint?



Regards 

Stefanie