Actually, I already answered this, but forgot to copy to the list: Here is my version:
Hervé Yes, this is defined in the documentation to the AMPS package for multiple alignment. You can read the description on-line here: http://www.compbio.dundee.ac.uk/manuals/amps/subsubsection3_18_2_5.html#SECTION00018250000000000000 AMPS together with its documentation can be downloaded from here: http://www.compbio.dundee.ac.uk/downloads/amps/ The blc file format is also used by some other older programs from my group (e.g. STAMP) since it allows additional information to be encoded after the sequences without destroying the ability for programs to read the amino acid sequences. For example, STAMP encodes information about structural similarity and AMAS outputs measures of conservation which are floating point numbers in an additional column. Geoff. On 22/10/2013 17:18, Jim Procter wrote: > Hi Hervé. > > The best documentation source is here: > http://www.compbio.dundee.ac.uk/manuals/scanps/subsection3_15_2.html > > Jalview supports access to any of the iterations - when reading a BLC > file, you can put a '#<iteration number>' after the filename to select > which iteration you want to import as an alignment. The BLC comment > section is imported and shown from the Alignment properties dialog. > > Is that sufficient ? Or should we encourage Geoff to put up a more > detailed example ;) > > Jim. > > Quoting "Hervé Ménager" <[email protected]>: > >> Hi Jim & al., >> I'm looking for any kind of documentation regarding the BLC alignment >> format which is supported by Jalview (I'm looking to register this >> format in EDAM ontology). Is there somewhere a specification for this >> format? >> Best, >> Hervé >> _______________________________________________ >> Jalview-discuss mailing list >> [email protected] >> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss >> > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss -- Geoff Barton Professor of Bioinformatics Head of Division of Computational Biology College of Life Sciences University of Dundee, Scotland, UK. [email protected] Tel:+44 1382 385860 www.compbio.dundee.ac.uk The University of Dundee is registered Scottish charity: No.SC015096 _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
