SimpleSearch database version information

 

15.08.2016  
GK release 28 (from 77,034 lines with genome hits: 23,582 gene hits, 14,235 CDSi hits). 
- Hit detection based on TAIR9 (still up-to-date) pseudochromosome sequences and Araport11 annotation.
- See FAQ 9 for our current definition of "gene hits". 
- 62.23 % of all A. thaliana nuclear genes are hit (gene hits, protein coding and RNA-encoding genes counted); 
- 75.42 % of A. thaliana nuclear protein coding genes are hit (gene hits, protein coding genes counted); 
- 51.87 % of A. thaliana nuclear protein coding genes are hit (CDSi hits counted); 
- 13967 lines had been sent to NASC on 2016-08-15. The current number of donated lines is presented here.
Note5: The Araport11 annotation contains 37,898 nuclear genes in total, including 27,445 nuclear protein coding genes.
Note6: Pseudogenes were now excluded as targets when evaluating gene hits and CDSi hits. The current release contains 1,062 lines with hits in the 941 pseudogenes reported by Araport11. 
13.05.2014  
GK release 27 (from 72,302 lines with genome hits: 22,515 gene hits, 14,253 CDSi hits). 
- Hit detection based on TAIR9 (= TAIR10) pseudochromosome sequences and TAIR10 annotation.
- See FAQ 9 for our current definition of "gene hits". 
- Pseudogenes included as target when evaluating gene hits and CDSi hits;
- 67.57 % of all A. thaliana genes are hit (gene hits, TS2TE hits and promoter hits counted); 
- 74.49 % of A. thaliana protein coding genes are hit (gene hits. TS2TE hits and promoter hits counted); 
- 52.39 % of A. thaliana protein coding genes are hit (CDSi hits counted); 
- 12,874 lines had been sent to NASC on 2014-05-13. 
10.04.2014  
GK release 26 (from 72,302 lines with genome hits: 21,453 gene hits, 13,435 CDSi hits). 
- Hit detection based on TAIR9 (= TAIR10) pseudochromosome sequences and TAIR10 annotation.
- See FAQ 9 for our current definition of "gene hits". 
- Pseudogenes included as target when evaluating gene hits and CDSi hits;
- 64.38 % of all A. thaliana genes are hit (gene hits, TS2TE hits and promoter hits counted); 
- 71.65 % of A. thaliana protein coding genes are hit (gene hits. TS2TE hits and promoter hits counted); 
- 49.39 % of A. thaliana protein coding genes are hit (CDSi hits counted); 
- 12,674 lines had been sent to NASC on 2014-04-10.
01.03.2012  
GK release 25 (from 72,064 lines with genome hits: 21,381 gene hits, 13,337 CDSi hits). 
- Hit detection based on TAIR9 (= TAIR10) pseudochromosome sequences and TAIR10 annotation.
- See FAQ 9 for our current definition of "gene hits". 
- Pseudogenes included as target when evaluating gene hits and CDSi hits;
- 64.2 % of all A. thaliana genes are hit (gene hits, TS2TE hits and promoter hits counted); 
- 71.4 % of A. thaliana protein coding genes are hit (gene hits. TS2TE hits and promoter hits counted); 
- 49.0 % of A. thaliana protein coding genes are hit (CDSi hits counted); 
- 10,239 lines had been sent to NASC on 2012-03-01.
07.03.2011  
GK release 24 (from 71,239 lines with genome hits: 18,908 gene hits, 13,038 CDSi hits).
- Hit detection based on TAIR9 pseudochromosome sequences and TAIR10 annotation.
- New definition of "gene hits": insertion between transcription start and polyA addition site (TS2pA - but see Note4 below/TS2TE). Only if this information is not available in the annotation data, 300 bp upstream of ATG to 300 bp downstream of STOP are considered. This change reduces the number of "gene hits". CDSi hit: insertion between ATG to STOP (CDS plus introns).
- Pseudogenes included as target when evaluating gene hits and CDSi hits;
- 56.3 % of all A. thaliana genes are hit (gene hits including TS2TE hits counted);
- 62.0 % of A. thaliana protein coding genes are hit (gene hits including TS2TE hits counted);
- 47.6 % of A. thaliana protein coding genes are hit (CDSi hits counted);
- 8,646 lines had been sent to NASC on 2011-03-07. 
Note2: The TAIR10 annotation dataset contains 33,602 genes in total, including 27.416 protein coding genes.
Note3: The GK release determines which lines and FSTs are available in SimpleSearch. If we produce new FSTs for our lines or even new lines, a new release is required to get these items into SimpleSearch. However, the data values for the items in the database are updated automatically once every 24 hrs from our internal LIMS (lab information managment system). This affects for example new segregation data, new NASC donations and NASC ID's, new confirmation sequences and so on. 
Note4: After the release 24 was made available, we changed the term TS2pA (from transcription start to polyA addition site) to TS2TE (from transcription start to transcript end) to also cover not polyadenylated ncRNA transcripts. 
04.08.2008  
GK release 23v2 (from 64244 lines with genome hits: 17,016 gene hits, 12,298 CDSi hits). 
- 6,018 lines have been sent to NASC.
30.11.2007  
GK release 23 (from 64,244 lines with genome hits: 17,016 gene hits, 12,298 CDSi hits).
- 5,551 lines have been sent to NASC .
20.03.2007  
GK release 22 (from 64,339 lines with genome hits: 17,018 gene hits, 12,301 CDSi hits).
- 4,293 lines have been sent to NASC.
25.06.2006
  
GK release 21 (from 63,812 lines with genome hits: 16,939 gene hits, 12,239 CDSi hits).
- 3,509 lines have been sent to NASC.
- New search interface allows searching for line ID or FST GenBank accession number.
- Genetic segregation and confirmation sequencing data included.
20.04.2006
  
GK release 20 (from 63,812 lines with genome hits: 16939 gene hits, 12,239 CDSi hits).
- 2,282 lines have been sent to NASC.
15.12.2005
  
GK release 19 (from 6,2697 lines with genome hits: 16,804 gene hits, 12,129 CDSi hits).
- 1,751 lines have been sent to NASC.
15.09.2005
  
GK release 18 (from 62,524 lines with genome hits: 16,782 gene hits, 12,112 CDSi hits).
- Information concerning lines transferred to NASC included (example: At2g31180).
- 712 lines have been sent to NASC.
01.02.2005
  
GK release 17 (from 61,768 lines with genome hits: 16,664 gene hits, 11,987 CDSi hits).
15.09.2004
  
GK release 16 (from 60,741 lines with genome hits: 16,558 gene hits, 11,883 CDSi hits).
- Hit detection based on TIGR sequence and BAC annotation v5.
01.05.2004
  
GK release 15 ** (from 60,527 lines with genome hits: 17063 gene hits, 12,304 CDSi hits).
15.03.2004
  
GK release 14 ** (from 55,138 lines with genome hits: 16214 gene hits, 11,560 CDSi hits).
01.02.2004
  
GK release 13 ** (from 52,250 lines with genome hits: 15,742 gene hits, 11,127 CDSi hits).
15.12.2003
  
GK release 12 ** (from 47,701 lines with genome hits: 14,914 gene hits, 10,425 CDSi hits).
05.10.2003
  
GK release 11 (from 44,358 lines with genome hits: 14,047 gene hits, 9,726 CDSi hits).
- Hit detection based on MAtDB release version 11092003.
01.08.2003
  
GK release 10 (from 36,486 lines with genome hits: 12470 gene hits, 8,493 CDSi hits).
01.07.2003
  
GK release 9 (from 36,206 lines with genome hits: 12382 gene hits, 8,425 CDSi hits).
01.06.2003
  
GK release 8 (from 35,302 lines with genome hits: 12191 gene hits, 8,270 CDSi hits).
01.03.2003
  
GK release 7 (from 31,734 lines with genome hits: 11350 gene hits, 7,599 CDSi hits).
15.02.2003
  
GK release 6 (from 26,375 lines with genome hits: 9,862 gene hits, 6,458 CDSi hits).
- New definition of "gene hits": insertion between 300 bp upstream of ATG to 300 bp downstream of stop. CDSi hit: insertion between ATG to stop (CDS plus introns).
- Hit detection based on MAtDB release version 11012003.
01.12.2002
  
GK release 5 (from 26,350 lines with genome hits: 8,230 gene hits, old definition).
01.10.2002
  
GK release 4 (from 24,138 lines with genome hits: 7,635 gene hits, old definition).
- Hit detection based on MAtDB release version 17092002.
01.09.2002
  
GK release 3 (from 22,825 lines with genome hits: 7,200 gene hits, old definition).
- A new page show the genes and FSTs graphically, search result page rearranged.
01.08.2002
  
GK release 2 (from 17,767 lines with genome hits: 5,835 gene hits, old definition).
- Hit detection based on MAtDB release version 26072002.
01.06.2002
  
Opening of the GABI-Kat homepage.
- GK release 1 (from 13,531 lines with genome hits: 4,642 gene hits, old definition).
- Hit detection based on MAtDB release version 11052002.

 

** Note1: There were 664 genes which were only annotated in TIGR and did not overlap with MAtDB gene annotations; these were incorporated in the dataset for hit detection.