SGPP Target Database Identifiers

When SGPP derived its original targets, genomes for the target organisms were still being sequenced and annotation was in its early stages. Many of the open reading frames were given temporary identifiers. This sequencing is now mostly complete, and annotation is nearing completion. Annotation will continue to be updated with new gene calls, sequence corrections, and function identification, but most gene identifiers are now supposed to be stable.

As of Sept. 2004, SGPP is in the process of updating its database and web page to reflect these new identifiers. Not all of the original ORFs match ORFs in the current sequence databases, and the link between old and new identifiers is not always clear. So the update is being done in several phases:

  1. New IDs added to searchable title line, for exact matches.
    COMPLETED SEPT. 16, 2004 for L. major

    For SGPP targets which have exact nucleotide sequence matches to current GeneDB ORFs (from the July 9, 2004 release) , the new GeneDB ID has been added to the title line. Searches done using the new identifier will find the right targets, with the new identifier as a prefix to the description field. For example, the title line which was previously:

    >Lmaj006828AAA GeneDB CHR6_tmp.82 CHR6_tmp.82 "coproporphyrinogen iii oxidase, aerobic, probable" PDB:1vju Ntag: MAHHHHHH
    is now:
    >Lmaj006828AAA GeneDB CHR6_tmp.82 CHR6_tmp.82 "LmjF06.1270 in 9 Jul 04 GeneDB; coproporphyrinogen iii oxidase, aerobic, probable" PDB:1vju Ntag: MAHHHHHH

    In this phase, the Database Identifier field shown on the web page still shows the original identifier, so that the field has a consistent meaning: ID at the time of selection. The web page will be altered to make this meaning clear.

  2. New IDs used as Database Identifier, for all matches.
    IN PROGRESS

    Once we have found the exact matches for our other target species, especially P. falciparum, and finished the process of finding the inexact matches and analyzing multiple matches and other ambiguities for L. major, we will replace the database identifiers used at the time of selection with the new stable identifiers, and change the web page to reflect this new meaning. The description (function) field will also be updated at this point.