- Bombyx mori comprehensive gene set was available in "Public Data" page.
- Total gene number was changed from 16,449 to 16,823 genes.
- Gene ID 'KBgn' was changed to 'BMgn' with the corresponding 6 numerals.
- Total 44 FLcDNA sequences were deleted due to a transposon and chimeras, or incomplete sequences.
- Clone names of 7 FLcDNA sequences were changed.
- "Genes" to be annotated by the 'Silkworm Genome Annotation Community' were added in the Keyword search and GBrowse of KAIKObase.
- Total 69,048 EST sequences were added in the EST database (KAIKOcDNA database).
- Total 15,887 full-length cDNAs derived from original full-length cDNAs and Bombyx mori mRNAs obtained from public database
were incorporated in the KAIKO full-length cDNA database (KAIKOcDNA database).
- 3' SAGE (Serial Analysis of Gene Expression) tags data derived from "posterior silkgland" (PSG) and derived from "middle silkgland" (MSG), both of which were the same developmental stage on fifth instar larval stage (Day 3') were integrated in GBrowse.
- "Locus" was deleted from the GBrowse data and the Keyword search data.
- KAIKObase with the above data was updated.
- A description of "full-length cDNA database (KAIKOcDNA database)" was added in the public data.
- EST database was updated in the Public data.
- KAIKObase version 3.1.0 with a whole set of full-length cDNA database and EST database was released.
- Full length cDNA and EST sequences were added in the KAIKOblast.
- Data of AyFib-GAL4 enhancer trap lines and Gene Trap lines were stored in Bombyx Trap DataBase (Release 2).
- Added trait markers of Bombyx Trap DataBase were stored in KAIKObase.
- Using information generated by BLASTp, the KAIKOGAAS predicted gene models (KAIKOGA) were separated into two groups: (1) a group including "No hits found" and sequences derived from transposon such as gag, integrase, reverse transcriptase, transposase etc., and (2) a group for other BLASTp results including the China gene models. The sequences derived from transposons can be shown by selecting the "KAIKOGAAS with TEs" track (check box) whereas the other gene models including the China gene models can be shown by selecting the "KAIKOGAAS without TEs" track (check box) in GBrowse.
- Links for SRS in the "KAIKOGAAS" database was modified.
- Links for "Genes" and "Transposons" in the "Public data" were modified.
- KAIKObase version 3.1.0 with following features was built:
1) Full length cDNA database was linked to KAIKObase.
2) EST database was linked to KAIKObase.
3) Full length cDNA and EST information was added.
4) Locus position was added.
- Gene models of "scaffold build2" by KAIKOGAAS were stored in the KAIKObase.
- KAIKOGA gene models on GBrowse of KAIKObase were linked to the KAIKOGAAS database.
- Gene models of KAIKOGAAS using "scaffold build2" sequences were stored in Annotation of Silkworm Genose Scaffolds of KAIKOGAAS database.
- KAIKOGAAS description was changed in Analysis tools page and KAIKOGAAS page.
- KAIKOGAAS link was added in Public data page.
- Publications were renewed in References.
- Top page of KAIKObase layout was changed.
- Silkworm gene model sequences were added to the KAIKOblast database.
- The function for sequence search corresponding to contig ID etc. in
KAIKOblast was deleted as it is already included in the keyword search
system of KAIKObase.
- The changes made in the previous version (ver.1) of KAIKObase can be
accessed from the KAIKObase page.
- Junk sequences (non-silkworm origin) in the KAIKOcontig.txt.gz
constructed in April 2004 were deleted.
- Junk sequences (non-silkworm origin) in "Assemble results of Japanese
WGS sequence, in Apr. 2004" of the KAIKOblast database were deleted.
- Contact e-mail address was changed on Bombyx Trap DataBase.
- "KAIKObase version2" with improved interface is added to the link page of "Bombyx Trap DataBase" and "KAIKO 2D DataBase (Proteome)". For more details, please visit "KAIKObase" home page.
- "Bombyx Trap DataBase" with information on reporter expressions and positions of transposon vectors (mutators) in transposon insertion lines (enhancer trap strains, or gene trap strains) is added to the "Public Data" page.
- "KAIKO 2D DataBase (Proteome)" has been updated from ver.1.00.a to ver.2.50.1 of Make2D-DB II package with the addition of gene models obtained from the joint collaboration of Japan and China.
- "Repeat sequence" can be downloaded from the "Genomic Sequences" page.
- "Repeat sequence" set was added to the KAIKOBLAST database.
- "Integrated sequence (integretedseq.txt.gz)" was replaced to "Genomic Sequences" page.
- Genomic Sequences page was renewed.
- Suffix "TA" and "PA" of gene IDs in the "glean_cds.txt.gz" and "glean_pro.txt.gz" files were deleted. These new files can be downloaded through the "Genomic Sequences" page.
- The silkworm genomic sequences obtained by the integration of WGS data of Japan and China can be downloaded as a set of the RAMEN assemble contigs, scaffolds, etc through the 'Public Data' page.
- "KAIKObase" is a unified silkworm genome database can be accessed through the KAIKObase page.
- Statistics of the assembled silkworm genome can be accessed through the Sequence page.
- "Bombmap" was moved to Public Data page.
- The assembled set (Unified scaffold+contig) was added to the KAIKOBLAST database.
- "Wild Silkbase: An EST database of wildmoths" site was added in the Link page.
- A linikage map constructed by a total of 1,755 SNPs was added to the Public Data page.
- KAIKOBLAST homepage was redesigned.
- BAC_end sequences were added to the KAIKOBLAST database.
- Two Fgenesh parameter (Apis mellifera, Tribolium castaneum) and GFSelectorK (Gene Function Selector for KAIKO) were added to the KAIKOGAAS.
- Japanese version of SGP homepage can be accessed through the top page.
- Inactive links were fixed.
- Publications were renewed in References.
- Information of 'Agreement for a joint research on silkworm genome information between Japan and China' was added to Sequences page.
- Silkworm proteome database (KAIKO 2DDB) can be accessed through the Public Data page.
- Publications were renewed in References.
- BAC End was added to the KAIKOBLAST database.
- Updated the Publication Papers in the References.
- Apis mellifera and Apis cerana partial cDNA sequences were added to the KAIKOBLAST database.
- The partial cDNA sequences were added to the KAIKOBLAST database. These sequences correspond to GenBank entries DN236876 - DN237878 submitted by the Zhejiang Sci-Tech University, China.
- The KAIKOBLAST was modified to facilitate more effective presentation of the BLAST results with a graphical viewer.
The How to use "KAIKOGAAS" on the web was revised in KAIKOGAAS in the Analysis Tools page.
The partial cDNA and the WGS scaffold sequences from the Chinese silkworm genome sequencing initiative were added to the KAIKOBLAST database. These sequences correspond to GenBank entries CH379587 - CH396048 and CK484630 - CK565104 submitted by the Southwest Agricultural University in Chongqing, China.
The WGS contig sequences from the Chinese silkworm genome sequencing initiative were added to the KAIKOBLAST database. These sequences correspond to GenBank entries AADK01000001 - AADK01066482 submitted by the Southwest Agricultural University in Chongqing, China.
- KAIKOBLAST: Drosophila melanogaster EST sequences from BDGP (13-Jul-2004) was added to BLAST's database.
- KAIKOBLAST: Drosophila melanogaster full-length cDNA sequences from BDGP DGC was updated to a data dated 15-Jul-2004.
- A system on which each user can perform a query using own sequence data was developed in KAIKOGAAS in the Analysis Tools page.
- Annotated contigs with lengths of more than 5Kb were added to the WGS RAMEN contig table in KAIKOGAAS in the Analysis Tools page.
- The How to use "KAIKOGAAS" on the web was revised in KAIKOGAAS in the Analysis Tools page.
- The KAIKOGAAS page was modified to facilitate more efficient access to annotation data. The tables with the list of annotated BAC clones and WGS contigs were transferred to a separate page. Links are provided through the KAIKOGAAS top page. The WGS contig table was also modified. Information on the presence or absence of ORFs for each contig is now included in the table.
- The RAMEN contig database with complementary sequences deleted using BLAST was unified.
- KAIKOGAAS: Kaiko Genome Automated Annotation System can be accessed through the Analysis Tools page.
- The results of sequence assembly using the RAMEN assembler and evaluation of whole-genome shotgun (WGS) sequence contigs based on the alignment of Bombyx non-redundant ESTs were reported in DNA Research and released in the 'Sequences' page.
- A database containing the whole-genome shotgun (WGS) sequence contigs and the tBLASTx program were added in KAIKOBLAST in the 'Analysis Tools' page.
- The silkworm genomic sequences can be downloaded as a set of the RAMEN assemble contigs through the 'Public Data' page.
- A search function for clone name / keyword in the silkworm EST database was added in the KAIKOcDNA of the 'Public Data' page. Homology value can be specified with specific options for NCBI-NR, Drosophila and C.elegans.
- We are pleased to announce the opening of the website for the Silkworm Genome Research Program (SGP) of the National Institute of Agrobiological Sciences (NIAS).