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Kluyveromyces lactis : Annotation Database entry page
Assembly status (15/10/03):
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Last info
Start browsing chromosomes:
(Initial settings will display maps starting at coordinate 1 with a range of 100000 nt)
Chromosome
Links (click to open)
Chromosome length
Database Status
Additional info
Chromosome I
1062590
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome II
1320834
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome III
1753957
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome IV
1715506
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome V
2234072
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome VI
2602197
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Mitochondria
40291
Open for annotation
- Predicted Mitochondrial tRNAs page
- Please note: annotation from H. Fukuhara has not been incorporeted yet into this database.
Jump directly to an item:
Type an item name:
e.g. type 'r_klactIV0761' . The map will be centered around the chosen item within a range selected in 'Diplay range'
Access to annotation data:
Annotation DataBase Search form : search currently available annotations and more in K.lactis database
Matched DataBase Search form : Explore K.lactis orfs hits in following public ressources:
- Similarity in SWISSPROT + trEMBL protein sequence database (May 2003 : sprot+trEMBL)
- Similarity in SWISSPROT protein sequence database ( release 41.O)
- Similarity in Yeast genome database (Inst. Pasteur)
- Similarity in C. albicans genome database (Assembly #6 of Stanford University)
- Pattern matches in Pfam (version 8) database using HMMER
- Similarity in KOG (7 eukaryal genomes) with function prediction
- Paralogs discovery (K. lactis self match with BLASTP)
K. lactis orfs hits in KOGs database : full listing digest of all hits with functional category guess
K. lactis annotation guidelines : a Shorthand "User Manual" for using K. lactis annotation database.
Everything you need to know to start annotating K. lactis genome at IGM Orsay.
Cross-reference page : K. lactis cross-reference of genes nomenclature in various databases
- 07/27/07 primary database is not in restricted area anymore
- 09/21/04 tRNA information added 21/09/04
- 09/20/04 intron/ exon information (from embl records)
- 09/17/04 genes cross-reference
- 29/01/04: "K. lactis annotation guidelines" page added
- 08/01/04: Installed K. lactis matches in public databases query page (Matched DataBase Search form )
- 01/02/04 : Added KOG hits full listing page and direct item map access utility (Jump).
- 12/27/03 : Installed annotation QueryPage (Annotation DataBase Search form)
- 12/24/03 : The basic DataBase setup for chromosomes I-VI and mitochondrial Genome is now finished . The databases are open for annotation
Auxilliary tools for efficient database access ( such as a "User Guide" , a query page for annotation data , and others ...) are now on my schedule and should be finished shortly.
Merry Chrismas and best wishes for the new year -Yvan
- 12/04/03 : The DataBase setup is almost finished.
I need a few days more to bring everything ready for interactive annotation - hopefully next week
In the meantime you can have a look and feel of the database design: pass your mouse over upper map elements, click buttons, play with the menus and see what happens - or does no happen !-
I will try as soon as possible to write a short "user guide" to help you .
If you encounter problems with a particular web browser drop me a mail to see if we can fix this. Recommended browsers are: Netscape (version 4.0 to 7 and more) , MSIE Explorer (version 4. up 5 and more ?), Safari, Mozilla , Camino (chimera). Others should also work, at least in their macOSX version.
This page is the starting point to anything related to annotation, and it will be enriched as information come in and new services become available (in particular a search form page)
Thank you for your patience - Yvan
Note: this is the final -last- sequence version. ORFs nomenclature has changed, as we don't maintain backward compatibility for this database. Accordingly, older versions numbering is DISCONTINUED (exept for chromosome I which was already finished in the previous release). Older sequence versions are left accessible as a convenience, but should not be used anymore.
Also note: preliminary (semi-automatic ) annotation performed on 10X 02/05/03 release has been incorporated in this database
Start browsing chromosomes:
(Initial settings will display maps starting at coordinate 1 with a range of 100000 nt)
Chromosome
Links (click to open)
Chromosome length
Database Status
Additional info
Chromosome I
1062590
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome II
1320834
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome III
1753957
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome IV
1715506
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome V
2234072
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Chromosome VI
2602197
Open for annotation
-New orfs extentions & additions incorporated 04/01/04
-intron/ exon information added 20/09/04
-tRNA information added 21/09/04
Mitochondria
40291
Open for annotation
- Predicted Mitochondrial tRNAs page
- Please note: annotation from H. Fukuhara has not been incorporeted yet into this database.
Jump directly to an item:
Type an item name:
e.g. type 'r_klactIV0761' . The map will be centered around the chosen item within a range selected in 'Diplay range'
Access to annotation data:
Annotation DataBase Search form : search currently available annotations and more in K.lactis database
Matched DataBase Search form : Explore K.lactis orfs hits in following public ressources:
- Similarity in SWISSPROT + trEMBL protein sequence database (May 2003 : sprot+trEMBL)
- Similarity in SWISSPROT protein sequence database ( release 41.O)
- Similarity in Yeast genome database (Inst. Pasteur)
- Similarity in C. albicans genome database (Assembly #6 of Stanford University)
- Pattern matches in Pfam (version 8) database using HMMER
- Similarity in KOG (7 eukaryal genomes) with function prediction
- Paralogs discovery (K. lactis self match with BLASTP)
K. lactis orfs hits in KOGs database : full listing digest of all hits with functional category guess
K. lactis annotation guidelines : a Shorthand "User Manual" for using K. lactis annotation database.
Everything you need to know to start annotating K. lactis genome at IGM Orsay.
Cross-reference page : K. lactis cross-reference of genes nomenclature in various databases
- 07/27/07 primary database is not in restricted area anymore
- 09/21/04 tRNA information added 21/09/04
- 09/20/04 intron/ exon information (from embl records)
- 09/17/04 genes cross-reference
- 29/01/04: "K. lactis annotation guidelines" page added
- 08/01/04: Installed K. lactis matches in public databases query page (Matched DataBase Search form )
- 01/02/04 : Added KOG hits full listing page and direct item map access utility (Jump).
- 12/27/03 : Installed annotation QueryPage (Annotation DataBase Search form)
- 12/24/03 : The basic DataBase setup for chromosomes I-VI and mitochondrial Genome is now finished . The databases are open for annotation
Auxilliary tools for efficient database access ( such as a "User Guide" , a query page for annotation data , and others ...) are now on my schedule and should be finished shortly.
Merry Chrismas and best wishes for the new year -Yvan - 12/04/03 : The DataBase setup is almost finished.
I need a few days more to bring everything ready for interactive annotation - hopefully next week
In the meantime you can have a look and feel of the database design: pass your mouse over upper map elements, click buttons, play with the menus and see what happens - or does no happen !-
I will try as soon as possible to write a short "user guide" to help you .
If you encounter problems with a particular web browser drop me a mail to see if we can fix this. Recommended browsers are: Netscape (version 4.0 to 7 and more) , MSIE Explorer (version 4. up 5 and more ?), Safari, Mozilla , Camino (chimera). Others should also work, at least in their macOSX version.
This page is the starting point to anything related to annotation, and it will be enriched as information come in and new services become available (in particular a search form page)
Thank you for your patience - Yvan
Note: this is the final -last- sequence version. ORFs nomenclature has changed, as we don't maintain backward compatibility for this database. Accordingly, older versions numbering is DISCONTINUED (exept for chromosome I which was already finished in the previous release). Older sequence versions are left accessible as a convenience, but should not be used anymore.
Also note: preliminary (semi-automatic ) annotation performed on 10X 02/05/03 release has been incorporated in this database