[BioPython] Clustalw pair wise alignment
Stefanie Lück
lueck at ipk-gatersleben.de
Wed Jan 30 10:24:55 UTC 2008
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
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