Does anyone know how to find codon usage from data in a genbank file or embl file.
Thanks Shakun On Fri, Oct 7, 2011 at 8:00 PM, <[email protected]>wrote: > Send Biojava-l mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/biojava-l > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Biojava-l digest..." > > > Today's Topics: > > 1. Re: losing meta-info after multiple sequence alignment > (Spencer Bliven) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 6 Oct 2011 11:29:06 -0700 > From: Spencer Bliven <[email protected]> > Subject: Re: [Biojava-l] losing meta-info after multiple sequence > alignment > To: Hannes Brandst?tter-M?ller <[email protected]> > Cc: "[email protected]" <[email protected]>, > Scooter Willis <[email protected]> > Message-ID: > <CA+P6arkEx4RTGWo=hadacx1v41fbv-cipuudq7llo+ooocx...@mail.gmail.com > > > Content-Type: text/plain; charset=UTF-8 > > I think that 1-based indexing was chosen because that's what's used in > genome databases like GenBank. Thus gene offsets from outside data sources > can be used directly without subtracting 1. That said, almost every time I > write code using sequences I get off-by-one errors, so I understand your > frustration. We should definitely improve documentation so that every > method > that takes 1-based indexes are clearly marked. > > -Spencer > > On Thu, Oct 6, 2011 at 03:37, Hannes Brandst?tter-M?ller < > [email protected]> wrote: > > > Thanks, I'll try to add what I find out. It's a wiki after all. I'll > > just ask the mailing list if things are unclear before I add stuff to > > the wiki. > > > > One thing that bugged me just now, and since I can't find documentation > on > > it: > > > > Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather > > un-java-like, especially since you just get an OutOfBoundsException, > > and the range is not specified in the javadoc, or I could not find it > > easily in the complex class hierarchy. > > > > Hannes > > > > 2011/10/6 Scooter Willis <[email protected]>: > > > Hannes > > > > > > As you can tell we need to improve the cookbook examples. Since you are > > > going through that process would welcome any contributions you can > make. > > > > > > Thanks > > > > > > Scooter > > > > > > On 10/6/11 4:07 AM, "Hannes Brandst?tter-M?ller" < > [email protected] > > > > > > wrote: > > > > > >>On Thu, Oct 6, 2011 at 09:32, Hannes Brandst?tter-M?ller > > >><[email protected]> wrote: > > >>> Hi again! > > >>> What I ran into now is that most of the meta-information of a > Sequence > > >>> seems to get lost during the MSA step. > > >> > > >>Okay, that was something caused by following another cookbook script > > >>(that, unfortunately, has absolutely no docs or comments) - I found > > >>the getOriginalSequence() method, can work with that. Thanks! > > >> > > >>Hannes > > >> > > >>_______________________________________________ > > >>Biojava-l mailing list - [email protected] > > >>http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > > > > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > > > > ------------------------------ > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > > End of Biojava-l Digest, Vol 105, Issue 5 > ***************************************** > Email Disclaimer: This email and all its contents are subject to the disclaimer at http://www.uom.ac.mu/emaildisclaimer _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
