Hi folks, I now received the answer from [EMAIL PROTECTED] (see below).
For my purposes, I conclude that don't need the "frame" value, especially since I use "blastn" as a program. It seems save to construct the (SeqSimilaritySearchSubHit's) query- and subject-strand values from the way the from- and to-values are ordered (ascending or descending). Jan answer from blast-help: -------8<---------------------------------------------- In our blast result, "Frame" refers to the translation orientation and frame since there are 6 possible ones with three from each strand. Their assigned value are +1, +2, +3, -1, -2, and -3. This is only relevant if query/db translation is involved (blastx, tblastn, tblastx). Since blast only reports local alignments, one may see multiple Frame with the same value mentioned, which may or may not cover the same area of the query or subject. One may be able to derive this using additional calculation from the from and to field along with the sequence length. However, BLAST calculates this out and presents it in a more straight forward manner. It is up to the user on whether to use it or not. -------------------------------->8--------------------- Am Tuesday 02 December 2003 23:57 schrieb Bobick, Stephen: > Interesting read. There are two sections worthy of comment: > >NCBI is not proposing a new data model, but is simply transliterating > >the data model we have used for the last decade into a different > > language > > for the > > >convenience of our users. ASN.1 has a number of specific data types such > > as INTEGER > > >or REAL numbers while XML has only strings, so our DTD automatically > > adds > > some > > >ENTITY definitions at the top which maps these numbers to strings. This > > mapping only > > >allows humans that read the DTD to see where numbers are expected; an > > XML > > validator > > >will not care what is there. > > Use of an XML Schema would allow the enforcement of data types. > > >Summary: > >While the effect of Roles, Scope, and Alternate Forms results in > > extensive > > >tags in the XML, it does accurately reflect the structure and use of the > > data. It allows > > >XML programs to capture as little or as much of the full data structure > > as they wish. > > I guess I fail to see the point of all this. How would a structure > resulting from the suggestions that I propose be "lossy" in any way? > > Stephen Bobick > > > -----Original Message----- > From: Michael E. Smoot [mailto:[EMAIL PROTECTED] > Sent: Tuesday, December 02, 2003 2:37 PM > To: Bobick, Stephen > Cc: [EMAIL PROTECTED] > Subject: Re: BLAST DTD (was RE: [Biojava-l] SeqSimilaritySearchSubHit - > Strand information) > > > > This page explains how the DTD's were created: > > http://www.ncbi.nlm.nih.gov/IEB/ToolBox/XML/ncbixml.txt > > The short version is that the DTD's are transliterations of their ASN.1 > data models. > > > Mike > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l -- Jan W�rthner Institute for Medical Microbiology Building 22.21 Heinrich-Heine-University Universit�tsstra�e 1 40225 Duesseldorf Tel. +49 (0) 211 81 12461 URL: www.medmikro.uni-duesseldorf.de _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
