Forum Topic: SGN data release notes

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SGN data release notes

This topic contains release notes for new SGN data releases.

This topic was started by Lukas Mueller.
Posted by Prabodh Trivedi (submitter) on 2013-02-20 23:31:36
 
We are working on Withania Gennomics and recently completed root and leaf transcriptomes of one of the chemotype using 454 plateform. SRA files (SRA053485; SRR 520142, SRR520143) have already been submitted to NCBI. We have assembled and annotated transcriptomes through TAIR10, NR, potato and tomato genomes. We would like to submit our contigs and singletons in fasta formation in SGN (withania) so that data is publically available for the community. Please let us know how we can submit the data in SGN.
Posted by Lukas Mueller (curator) on 2011-02-15 10:29:41
 
New maps added to SGN

Four new maps have been added to SGN: The maps of two Nicotiana species, a potato map, and a tomato map. Many thanks to the submitters, Feinan Wu, Dan Bolser, David Francis and their colleagues for making the maps available. [January 6, 2011]
Posted by Jerome Collemare on 2010-08-19 10:43:31
 
Dear all,

I ran a Blast with my favorite protein on the tomato WGS scaffolds 2.30 database and got a list of hits with the name of corresponding scaffolds. When I click on the name I got a new page with the nucleotide sequence corresponding to the result of my query and I have the position on the scaffold. How can I see this sequence in the genome browser? I tried to search using the sequence ID I was given, but it did not work.

Thank you for any help!
Jerome
Posted by Diamond Sinha on 2010-02-28 13:25:22
 
I want to know virus resistance gene reference/accession in tomato.
Posted by Pooja Jain on 2010-02-02 07:32:34
 
Hi,

I have a list of SGN-U###### Unigene ids of Tomato from an out-of-date build, Tomato 200607 #1. I would like to have their mapping to the current build Tomato 200607 #2. Could anyone please tell me if such a mapping available to download or there is any conversion tool just as SGN <=> TIGR ? Is there any parse-able file to map the two builds ?

Also some of the SGN-IDs from the old build is now split into two in the new build. In that case what could be the suggestion for an appropriate mapping.

Thank you.

-Pooja
Posted by Aureliano Bombarely (curator) on 2008-09-23 10:39:10
 
New protein predictions available for Nicotiana tabacum unigene build#2 (date=2008_07_17) with 84602 sequences.

-by estscan= 80117 sequences
-by longest6frame= 87142 sequences
Posted by Naama Menda (curator) on 2008-09-11 12:51:37
 
Added a new pepper EMS mutants population, with 629 accession and 169 associated images.
Data was submitted by Ilan Paran, Volcani ARO, Israel.

Posted by Naama Menda (curator) on 2008-09-09 15:07:46
 
1189 SGN tobacco loci are now linked with 1599 SGN Nicotiana tabacum Unigenes.
Cross links are available on both locus and unigene pages.
Posted by Aureliano Bombarely (curator) on 2008-09-04 12:32:22
 
New unigene build for Ipomoea batatas:

Build_Number=1 (unigene_build_id=40);
Date=2008_05_27;

Statistics:

- Members: 19400.
- Unigenes: 7862.
- Singlets: 4987.
- Contigs: 2875.
Posted by Aureliano Bombarely (curator) on 2008-09-04 12:30:42
 
New unigene build for Nicotiana sylvestris:

Build_Number=1 (unigene_build_id=41);
Date=2008_06_05;

Statistics:

- Members: 7890.
- Unigenes: 6300.
- Singlets: 5383.
- Contigs: 917.
Posted by Aureliano Bombarely (curator) on 2008-09-04 12:28:43
 
New unigene build for Nicotiana benthamiana:

Build_Number=1 (unigene_build_id=43);
Date=2008_08_04;

Statistics:

- Members: 55014.
- Unigenes: 16024.
- Singlets: 5819.
- Contigs: 10205.
Posted by Naama Menda (curator) on 2008-09-04 08:38:40
 
Added 77 PO growth-stage annotations to 67 tobacco loci
and 1311 PO anatomy annotations for 391 tobacco loci.

These annotations were imported from TAIR based on putative arabidopsis orthologs inferred from TBLASTX results.
Posted by Aureliano Bombarely (curator) on 2008-09-03 17:24:49
 
New unigene build for Nicotiana tabacum:

Build_Number=2 (unigene_build_id=43);
Date=2008_07_17;

Statistics:

- Members: 239761.
- Unigenes: 84602.
- Singlets: 53906.
- Contigs: 30696.
Posted by Naama Menda (curator) on 2008-09-03 14:36:31
 
Added 6171 GO annotations to 1304 Tobacco genes.
These annotations were imported from TAIR based on best TBLASTX match to the corresponding tobacco locus sequences.
Posted by Naama Menda (curator) on 2008-09-02 13:03:38
 
Inserted 1521 new tobacco loci, 652 locus aliases
1 alleles, 1 marker association, 2736 locus-dbxref associations
**624 new pubmed references were associated with tobacco loci.
Posted by Aureliano Bombarely (curator) on 2008-09-02 11:14:08
 
New sequences for SGN database and ftp site:

* Organism: Nicotiana tabacum.
* Source: GenBank, S.Coates (ATC) contribution and TGI (Tobacco Genome Intiative) downloads.
* Sequences stored:
- OLD: 87 287 seq
- NEW: 173 227 seq
- TOTAL: 260 514 (239 798 sequences processed).
- average sequence length: 620.72 bp (range from 100 bp to 7676 bp)
* Libraries stored:
-OLD: 19.
-NEW: 20
-TOTAL: 39

* Ftp files stored as: /mRNA_by_library and /mRNA_by_organism:
- nicotiana_tabacum_est_by_library_2008_07_14.membermap.tab (library, SGN-E and gb_accession)
- nicotiana_tabacum_mRNA_2008_07_14.qual.fasta (239 798 sequences)
- nicotiana_tabacum_mRNA_2008_07_14.seq.fasta (239 798 sequences)

* Notes: Also stored 243 849 GenBank accessions.
Posted by Aureliano Bombarely (curator) on 2008-08-27 19:21:00
 
New sequences for SGN database and ftp site:

* Organism: Nicotiana benthamiana.
* Source: GenBank and TGI (Tobacco Genome Intiative) downloads
* Sequences stored:
- 56 124 (55 031 sequences processed).
- average sequence length: 577.96 bp (range from 100 bp to 7230 bp)
* Libraries stored: 8.

* Ftp files stored as: /mRNA_by_library and /mRNA_by_organism:
- nicotiana_benthamiana_est_by_library_2008_08_25.membermap.tab (library, SGN-E and gb_accession)
- nicotiana_benthamiana_mRNA_2008_08_25.qual.fasta (55 031 sequences)
- nicotiana_benthamiana_mRNA_2008_08_25.seq.fasta (55 031 sequences)

* Notes: Also stored 42 850 GenBank accessions.
Posted by Aureliano Bombarely (curator) on 2008-08-27 18:15:35
 
New sequences for SGN database and ftp site:

* Organism: Nicotiana sylvestris.
* Source: GenBank.
* Sequences stored:
- 8 677 (7 894 sequences processed).
- average sequence length: 342.55 bp (range from 99 bp to 5777 bp)
* Libraries stored: 2.

* Ftp files stored as: /mRNA_by_library and /mRNA_by_organism:
- nicotiana_sylvestris_est_by_library_2008_08_25.membermap.tab (library, SGN-E and gb_accession)
- nicotiana_sylvestris_mRNA_2008_08_25.qual.fasta (7 894 sequences)
- nicotiana_sylvestris_mRNA_2008_08_25.seq.fasta (7 894 sequences)

* Notes: Also stored 8 677 GenBank accessions.
Posted by Aureliano Bombarely (curator) on 2008-08-27 16:47:34
 
New sequences for SGN database and ftp site:

* Organism: Ipomoea batatas.
* Source: GenBank.
* Sequences stored:
- 19 686 (19 411 sequences processed).
- average sequence length: 558.21 bp (range from 100 bp to 3240 bp)
* Libraries stored: 12.

* Ftp files stored as: /mRNA_by_library and /mRNA_by_organism:
- ipomoea_batatas_est_by_library_2008_08_15.membermap.tab (library, SGN-E and gb_accession)
- ipomoea_batatas_mRNA_2008_08_15.qual.fasta (19 411 sequences)
- ipomoea_batatas_mRNA_2008_08_15.seq.fasta (19 411 sequences)

* Notes: Also stored 19 686 GenBank accessions.
Posted by Naama Menda (curator) on 2008-06-30 12:57:03
 
The SGN locus database is updated:
249 existing tomato loci were updated with 249 associated GenBank sequences,
74 Plant Ontology and
228 Gene Ontology electronic annotations (inferred from best sequence match to annotated arabidopsis genes).

Posted by Naama Menda (curator) on 2008-05-07 16:12:24
 
The SGN locus database is updated with additional 515 tomato loci, 341 associated publications, 610 accessions from GenBank, 997 Plant Ontology and 2398 Gene Ontology electronic annotations (inferred from best sequence match to annotated arabidopsis genes).
Posted by Lukas Mueller (curator) on 2008-05-07 10:06:35
 
A set of 44 datura genes was added to the SGN locus database. These genes come from 67 genbank accessions, with 25 publications associated and 202 GO and 66 PO electronic annotations that came from best blast match to arabidopsis.
Posted by Lukas Mueller (curator) on 2008-05-07 10:04:58
 
We have added 356 *petunia* loci to the SGN genes database:
[url]http://www.sgn.cornell.edu/search/locus_search.pl?w8e4_common_name=Petunia[/url]

Petunia loci have associated sequences (SGN unigenes and GenBank
accessions), publications, biochemical pathways, gene-network
relationships, and Gene and Plant Ontology annotations.

You may be already familiar with the SGN's effort to create a medium and
tools for the solanaceae research community to annotate their
genes and phenotypes, that way ensuring the quality of data in the
database is as accurate, current and accessible as possible.

You are encouraged to review these genes, submit your comments and
requests, upload additional information to existing genes, and submit
new ones if you cannot find your favorite gene (logging in is required
for data submission).

For more information, please see SGN's user annotations guidelines:
http://www.sgn.cornell.edu/phenome/
Please do not hesitate to contact SGN (sgn-feedback@sgn.cornell.edu)
with any questions you may have!

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