TOMATOMICS

tomatomics  The Tomato Integrated Database

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Amino Acid Sequences of HTCs predicted by InterProScan
File Date File size Content
HTC13227_translate_ipr.amino.gz 2015/04/07 8.45MB The amino acid sequences of HTCs were predicted by the InterProScan Search.
It contains translation in all six reading frames.
The header line for each sequence in the FASTA file shows the frame (frame 1 to frame 6) and coding region,

e.g., "frame 3, ORF 1" means the +2 frame and the first region, "frame 4, ORF 2" means the -1 frame and the second region.
SNP
File Date File size Content
SNP_list_Heinz_1706_vs_Micro-Tom.txt.tar.gz 2013/06/07 27.9MB Table about predicted SNP,between Heinz 1706 genome and Micro-Tom genome, each column is as below.

1. Chromosome Number
2. SNP Position on Chromosome
3. Heinz 1706 allele
4. Micro-Tom allele
SNP_list_Heinz_1706_vs_Micro-Tom.vcf.tar.gz 2013/11/14 136MB
InDel
File Date File size Content
InDel_list_Heinz_1706_vs_Micro-Tom.txt.tar.gz 2013/06/07 18.7MB Table about predicted InDel,between Heinz 1706 genome and Micro-Tom genome, each column is as below.

1. Chromosome Number
2. InDel Position on Chromosome
3. Insertion/Deletion
4. InDel Length
5. InDel Nucleic Acid Sequence
6. Calculation Method (Pileup/Mplileup)
7. Number of Gene Which Contains InDel
8. Structure of The Gene that Contains InDel
9. Gene Module ID in ITAG2.3
InDel_list_Heinz_1706_vs_Micro-Tom.vcf.tar.gz 2013/11/14 27MB
Correspondence Table Heinz 1706 vs MicroTom
File Date File size Content
Heinz_1706_id_vs_Micro-Tom_EST_id.txt.tar.gz 2015/01/28 4.4MB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, INSDC Accession numbers, and Micro-Tom EST names, each column is as below.

1. Micro-Tom EST name
2. INSDC Accession number
3. Heinz 1706 Transcriptome ID in ITAG2.5

Heinz_1706_id_vs_Micro-Tom_HTC_id.txt.tar.gz 2015/01/28 0.41MB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, INSDC Accession numbers, and Micro-Tom HTC names, each column is as below.

1. Micro-Tom HTC name
2. INSDC Accession number
3. Heinz 1706 Transcriptome ID in ITAG2.5

Correspondence Table Heinz 1706 vs SGN EST (Solanum lycopersicum)
File Date File size Content
Heinz_1706_id_vs_R11_12andR11_13_EST_id.txt.tar.gz 2015/01/28 0.38MB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, R11_12 and R11_13 clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. R11_12 and R11_13 EST ID (SGN EST ID)
2. R11_12 and R11_13 clone name
3. INSDC Accession number
4. Heinz 1706 Transcriptome ID in ITAG2.5

Heinz_1706_id_vs_TA496_EST_id.txt.tar.gz 2015/01/28 4.4MB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, TA496 clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. TA496 EST ID (SGN EST ID)
2. TA496 clone name
3. INSDC Accession number
4. Heinz 1706 Transcriptome ID in ITAG2.5

Heinz_1706_id_vs_Rio_Grande_PtoR_EST_id.txt.tar.gz 2015/01/28 0.34MB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, Rio Grande PtoR clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. Rio Grande PtoR EST ID (SGN EST ID)
2. Rio Grande PtoR clone name
3. INSDC Accession number
4. Heinz 1706 Transcriptome ID in ITAG2.5

Heinz_1706_id_vs_West_Virginia_106_EST_id.txt.tar.gz 2015/01/28 21.3KB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, West Virginia 106 clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. West Virginia 106 EST ID (SGN EST ID)
2. West Virginia 106 clone name
3. INSDC Accession number
4. Heinz 1706 Transcriptome ID in ITAG2.5

Heinz_1706_id_vs_cultivar_unknown_EST_id.txt.tar.gz 2015/02/03 1.1MB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, cultivar unkown clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. cultivar unkown EST ID (SGN EST ID)
2. cultivar unkown clone name
3. INSDC Accession number
4. Heinz 1706 Transcriptome ID in ITAG2.5

Correspondence Table Heinz 1706 vs SGN EST (Solanum pennellii)
File Date File size Content
Heinz_1706_id_vs_LA716_EST_id.txt.tar.gz 2015/02/03 94.1KB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, LA716 clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. LA716 EST ID (SGN EST ID)
2. LA716 clone name
3. INSDC Accession numer
4. Heinz 1706 Transcriptome ID in ITAG2.5

Heinz_1706_id_vs_TA56_EST_id.txt.tar.gz 2015/02/03 0.16MB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, TA56 clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. TA56 EST ID (SGN EST ID)
2. TA56 clone name
3. INSDC Accession numer
4. Heinz 1706 Transcriptome ID in ITAG2.5

Correspondence Table Heinz 1706 vs SGN EST (Solanum habrochaites)
File Date File size Content
Heinz_1706_id_vs_LA1777_EST_id.txt.tar.gz 2015/02/03 75.6KB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, LA1777 clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. LA1777 EST ID (SGN EST ID)
2. LA1777 clone name
3. INSDC Accession number
4. Heinz 1706 Transcriptome ID in ITAG2.5

Heinz_1706_id_vs_PI126449_EST_id.txt.tar.gz 2015/02/03 0.16MB Table about correspondence between Heinz 1706 transcript IDs in ITAG2.5, PI126449 clone names, INSDC Accession numbers, and SGN EST IDs, each column is as below.

1. PI126449 EST ID (SGN EST ID)
2. PI126449 clone name
3. INSDC Accession number
4. Heinz 1706 Transcriptome ID in ITAG2.5