tag:blogger.com,1999:blog-21289662.post8617627725846602698..comments2023-09-26T01:39:21.395-07:00Comments on Bioinformatics: needleman-wunsch global sequence alignment -- updates and optimizations to nwalignbrentphttp://www.blogger.com/profile/12236821145627337774noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-21289662.post-84527364264105265842010-04-25T20:17:18.971-07:002010-04-25T20:17:18.971-07:00@Meric also check the docs on this page: http://py...@Meric also check the docs on this page: http://pypi.python.org/pypi/nwalign/<br /><br />there's a score_alignment() function that will tell you the score.brentphttps://www.blogger.com/profile/12236821145627337774noreply@blogger.comtag:blogger.com,1999:blog-21289662.post-1422959964782720142010-04-25T20:16:11.977-07:002010-04-25T20:16:11.977-07:00@Meric, you'll want to install from pypi:
http...@Meric, you'll want to install from pypi:<br />http://pypi.python.org/pypi/nwalign/<br /><br />or use mercurial and get it from bitbucket:<br />http://bitbucket.org/brentp/biostuff/srcbrentphttps://www.blogger.com/profile/12236821145627337774noreply@blogger.comtag:blogger.com,1999:blog-21289662.post-55945418969723025082010-04-25T18:36:35.435-07:002010-04-25T18:36:35.435-07:00one more thing
I get his error error: Can't ...one more thing <br /><br />I get his error error: Can't download http://bpbio.googlecode.com/svn/trunk/nwalign/: 404 Not Found<br /><br />when I want to use easy_installMericnoreply@blogger.comtag:blogger.com,1999:blog-21289662.post-71008770901217082972010-04-25T18:35:37.608-07:002010-04-25T18:35:37.608-07:00one more thing,
sudo easy_install -UZ http://bpbio...one more thing,<br />sudo easy_install -UZ http://bpbio.googlecode.com/svn/trunk/nwalign/<br />this is giving the following error<br /><br />error: Can't download http://bpbio.googlecode.com/svn/trunk/nwalign/: 404 Not FoundMericnoreply@blogger.comtag:blogger.com,1999:blog-21289662.post-29992148655757270762010-04-25T18:19:56.464-07:002010-04-25T18:19:56.464-07:00Hi
thank you for the code.
however I need a simila...Hi<br />thank you for the code.<br />however I need a similarity score (a percentage value) between two sequences. I have another code that will do that for me after your alignment, however I was wondering if your code will give me something like that?<br />thank you for sharing your work.mericnoreply@blogger.comtag:blogger.com,1999:blog-21289662.post-52470125212370149062010-01-22T07:33:02.324-08:002010-01-22T07:33:02.324-08:00hi carles, you are correct, that is a bad alignmen...hi carles, you are correct, that is a bad alignment, someone else has reported this same thing. i will have this fixed in the next release. hopefully that will be next week.<br />meanwhile, yes, i suggest you specify a matrix.brentphttps://www.blogger.com/profile/12236821145627337774noreply@blogger.comtag:blogger.com,1999:blog-21289662.post-37841085705731506222010-01-22T06:11:10.404-08:002010-01-22T06:11:10.404-08:00Hi.
Thanks a lot for your program, it saved me lo...Hi.<br /><br />Thanks a lot for your program, it saved me lot of trouble.<br /><br />I found a situation where I got a non-satisfactory result, but as I'm inexperienced in alignments I'm not sure it's incorrect.<br /><br />nwalign.global_align("FFLYVLEMVSKPMI","FFLYVG")<br /><br />Result:<br /><br />('FFLYVLEMVSKPMI', 'FFLY----V----G')<br /><br />When I was expecting 'FFLYV--------G' for the second sequence.<br /><br />It doesn't change a thing if I specify a gap_open or gap_extend penalty, or match score. On the other hand, if a use the BLOSUM62 matrix everything is fine. BTW, I've tried 0.3 and 0.3.1<br /><br />I'm I doing something wrong?<br /><br />Thanks for your work.<br /><br />Carles.Carlesnoreply@blogger.com