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PlantGDB Download Portal
Version Number: 157a
This download page contains the Oryza_sativa__indica_cultivar_group_ assembly results (assembled by PlantGDB). For more information about the assembly, please see EST assembly information page.
More about download files...
Explanation of files available for download
-
Oryza_sativa__indica_cultivar_group_.mRNA..PUT.fasta.bz2: .bz2 compressed putative unique transcript sequences in FASTA format.
- Oryza_sativa__indica_cultivar_group_.PUT.Similar_Protein.txt.bz2: .bz2 compressed top three matched BLASTX output (putative unique transcript sequences as query BLASTXing against UniProt protein database) with the following 15 columns.
- Organism of query sequence
- PUT sequence ID
- Matched protein ID
- Percentage identity in the BLAST alignment
- Alignment length
- Number of mismatch in the BLAST alignment
- Number of gap opening in the BLAST alignment
- The start position of the query sequence in the alignment
- The end position of the query sequence in the alignment
- The start position of the subject sequence in the alignment
- The end position of the subject sequence in the alignment
- E_Value
- Bit_Score
- Description of the protein
- Species name of the protein
-
Oryza_sativa__indica_cultivar_group_.PUT.fasta.blastxOutput.bz2: .bz2 compressed BLASTX output (putative unique transcript sequences as query BLASTXing against UniProt protein database).
- Oryza_sativa__indica_cultivar_group_.PUT_member.txt.bz2: .bz2 compressed tab-delimited file describing the coordinates (strand orientation, start position, end postion) of each member mRNAs with respect to the PUT into which they have been assembled.
- Oryza_sativa__indica_cultivar_group_.alignment.txt.bz2: .bz compressed tab-delimited file with the following 8 columns.
- Organism
- PUT ID
- Member mRNA ID
- Strand orientation of the member mRNA in the assembly
- The base position of the PUT where the member mRNA starts
- The base position of the PUT where the member mRNA ends
- The base position of the member mRNA where the mRNA's contribution to the PUT sequence starts
- The base position of the member mRNA where the mRNA's contribution to the PUT sequence ends
Files for Download
Tips for using the Download Portal:
Sequence
- Choose sequence type from left menu
- Select or enter species
- Use links to either move down in the directory structure or upload files to your browser.
- To save files to your local disk, right mouse click and "Save Target As...").
- To uncompress .bz2 files, use command bunzip2 filename.bz2 on Unix/Linux
Databases
- Select PlantGDB or any xGDB (for genome browser data) from the menu at left
- Directories contain MySQL table structures (*.sql files) and table data (*.txt files) as generated by a MySQL "dump" command.
- To save files to your local disk, right mouse click and "Save Target As...").
- To uncompress .bz2 files, use command bunzip2 filename.bz2 on Unix/Linux
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