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PlantGDB Download Portal
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This download page contains the Pinuspinaster 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
-
Pinuspinaster.mRNA..PUT.fasta.bz2: .bz2 compressed putative unique transcript sequences in FASTA format.
- Pinuspinaster.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
-
Pinuspinaster.PUT.fasta.blastxOutput.bz2: .bz2 compressed BLASTX output (putative unique transcript sequences as query BLASTXing against UniProt protein database).
- Pinuspinaster.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.
- Pinuspinaster.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
- File or Directory Name / Date / File Size
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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