[Biojava-l] Globla Sequence Alignment

Andreas Dräger andreas.draeger at clever-telefonieren.de
Sun Aug 28 11:08:42 EDT 2005


I just implemented the Needleman-Wunsch-Algorithm and an object for 
handling substitution matrices like BLOSSUM, PAM, GONNET and so on. It 
parses a matrix file and provides a method to get the costs for changing 
Symbol A to Symbol B. This is realized by two hashes and a private 
int[][] matrix.
If NeedlemanWunsch gets equal weights for gap opening and gap extension 
it won't consider affine gap penalties, whereas otherwise it will, which 
needs three times more memory.

Andreas Dräger

-------------- next part --------------
A non-text attachment was scrubbed...
Name: NeedlemanWunsch.java
Type: text/x-java
Size: 14813 bytes
Desc: not available
Url : http://portal.open-bio.org/pipermail/biojava-l/attachments/20050828/c60b3c62/NeedlemanWunsch-0001.bin
-------------- next part --------------
A non-text attachment was scrubbed...
Name: SubstitutionMatrix.java
Type: text/x-java
Size: 12573 bytes
Desc: not available
Url : http://portal.open-bio.org/pipermail/biojava-l/attachments/20050828/c60b3c62/SubstitutionMatrix-0001.bin

More information about the Biojava-l mailing list