tag:blogger.com,1999:blog-36768584.post2094021499517588693..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: The good, bad & missing from Bio* libraries?Keith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-36768584.post-21982281498259826252014-07-25T04:36:56.992-04:002014-07-25T04:36:56.992-04:00I think BioPerl has decent Dynamic Programming mod...I think BioPerl has decent Dynamic Programming module called Bio::Tools:dpAlign. It implements Miller-Myers algorithm which is analytically equivalent to Smith-Waterman but runs faster and consumes only linear memory space. Maybe you can check it out and port it to Julia?Geneticist from the Eastnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-75192392244390211892014-07-01T16:06:01.218-04:002014-07-01T16:06:01.218-04:00It would be nice to support gzip format without th...It would be nice to support gzip format without the need to specify it. In BioPerl they suggest using:<br /><br />-file => 'gunzip -c file.name |'<br /><br />But that is awkward and prone to breakage if your gunzip is not in your path. I know that it is possible to write programs that examine the gzip'ness of a file and deal with it automatically.<br />Rickhttps://www.blogger.com/profile/09945270829932237628noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-74709969613060328492014-07-01T06:35:55.657-04:002014-07-01T06:35:55.657-04:00You probably already know, but in Bio::Seq you can...You probably already know, but in Bio::Seq you can use trunc() instead of subseq() to return a sequence object...<br /><br />Totally agree about BioPerl's handling of alignment objects. I'm about to have to use it again for a project and I'm dreading it.<br /><br />Personally, I'd like to see more robust handling of the GenBank format. It's stupid and archaic and loosely structured at best, but until we get our coworkers away from commercial packages, it's the rich sequence format we're stuck with.Scholanderhttps://www.blogger.com/profile/12933906551105000203noreply@blogger.com