Data Sets Available from BioViz
The Bioviz site delivers data via two main mechanisms: our Bioviz Quickload site and our Bioviz DAS/2 servlet.
| Data Source | Description |
|---|---|
| Bioviz Quickload | Quickload offers entire genome-scale data files, which you can access via IGB or download from our Web site directly. To view the Quickload data files, visit the publicly-accessible Quickload directories on our Web site. |
| Bioviz DAS2 |
DAS stands for Distributed Annotation System. We use DAS to deliver data sets, such as EST alignments, that are too large to load into IGB all at once. The DAS server allow incremental data loading into IGB. Instead of loading an entire data set, IGB instead requests data that cross a given query region.
When you click the Refresh Data button in IGB, IGB asks our Bioviz DAS2 server for data sets with Load Mode set to Region in View. If the data sets have any data that overlap the region currently in view, then IGB will retrieve those data from the server and display them. If not, nothing will appear. However, to remind you that you've made the request, IGB changes the background color for regions and tracks where you requested the data. |
Most of the time, you will not need to think about whether IGB is loading data via DAS2 or Quickload. If you are curious about DAS2 or Quickload, or if you would like to set up your own DAS2 or Quickload servers, you can read more about them on the Genoviz Web site or contact us for more information.
To find out more about the data sets we deliver from the BioViz Quickload and Bioviz DAS servers, read on:
Arabidopsis thaliana (Genome Version: A_thaliana_TAIR9)
Bioviz Quickload Data Sets include gene annotations from the TAIR9 annotation release from summer, 2009. For details, see the table below:
| Data Set | Gene Model Type | Description (Adapted from this TAIR Help Page) |
|---|---|---|
| TAIR9 ALL | All gene models | All gene models from TAIR, including protein coding and non-coding genes |
| TAIR9 mRNA | protein coding | A gene model whose product is a transcript which is subsequently translated into a protein. |
| TAIR9 tRNA | pre trna | A gene model in which the primary product of transcription codes for transfer RNAs (t-RNA). The pre-tRNA of prokaryotes and eukaryotes has extra nucleotides at the 5' and 3' extremities and in some eukaryotic pre-tRNAs introns are also present. Maturation of tRNA precursors is a multistep enzymatic process consisting of nucleolytic size reducing reactions and of nucleotide modifications. |
| TAIR9 miRNA | microRNA | MicroRNAs are regulatory RNAs with a mature length of ~21-nucleotides that are processed from hairpin precursors by Dicer-like enzymes. MicroRNAs can negatively regulate gene expression by attenuating translation or by directing mRNA cleavage. For an example, see gene model AT3G04765.1 |
| TAIR9 ncRNA | non-coding RNA | A transcribed gene about which little is known, including whether or not its transcribed RNA is translated into protein via the usual mechanism. For an example, see gene model AT3G06125.1 |
| TAIR9 snRNA | small nuclear RNA | Also known as snRNA. Small nuclear RNA (snRNA) is the name used to refer to a number of small RNA molecules found in the nucleus. These RNA molecules are important in a number of processes including RNA splicing (removal of the introns from hnRNA) and maintenance of the telomeres, or chromosome ends. They are always found associated with specific proteins and the complexes are referred to as small nuclear ribonucleoproteins (SNRNP) or sometimes as snurps. |
| TAIR9 snoRNA | Small nuclear RNAs | Small nuclear RNAs (snoRNA) that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P. |
| TAIR9 rRNA | ribosomal rna | The transcribed product of ribosomal DNA, also known as rRNA. These rRNAs are part of the ribosome. |
| TAIR9 pseudogene | pseudogene | A gene model that represents a sequence of DNA that is very similar to a normal gene but that has been altered slightly so it is not expressed. Such genes were probably once functional but over time acquired one or more mutations that rendered them incapable of producing a protein product.The transcribed product of ribosomal DNA, also known as rRNA. These rRNAs are part of the ribosome. |
Bioviz DAS2 Data Sets include genomic alignments of ESTs and cDNAs from GenBank. We used blat (default settings) to align the ESTs and cDNAs onto the TAIR9 genome. Only alignments in which the query sequence (EST or cDNA) aligned with 95% identify or better and where the alignment included 90% of the query sequence were kept.
Next, we sub-divided the alignments into two groups: The single map (sm) groups include sequences that aligned to one unique location in the genome. The multiple map groups (mm) include sequences that map onto more than one location in the genome. The latter group is useful mainly for visualizing highly-similar, duplicate regions in the genome.
| Data Set | Description |
|---|---|
| EST (single map) | Genome alignments for Arabidopsis ESTs from Genbank dbEST database aligned to the genome using the procedure described above. The data were from The ESTs data set included approximately 1.5 million ESTs and was obtained from PlantGDB in the summer of 2009. Each sequence aligned just once under criteria described above. |
| EST (spliced, single map) | The subset of the EST (single map) alignments that included putative introns, e.g., gaps in the query greater than or equal to 30 bases. |
| EST (multiple map) | The same as the EST (single map) data set described above, except that each EST in this data set aligned more than once under the stringency criteria described above. |
Arabidopsis thaliana (Genome Version: A_thaliana_Apr_2008)
Bioviz Quickload Data Sets include gene annotations from the TAIR8 annotation release from summer, 2008. For details, see the table below:
| Data Set | Gene Model Type | Description (Adapted from this TAIR Help Page) |
|---|---|---|
| TAIR8_mRNA | protein coding | A gene model whose product is a transcript which is subsequently translated into a protein. |
| TAIR8_tRNA | pre trna | A gene model in which the primary product of transcription codes for transfer RNAs (t-RNA). The pre-tRNA of prokaryotes and eukaryotes has extra nucleotides at the 5' and 3' extremities and in some eukaryotic pre-tRNAs introns are also present. Maturation of tRNA precursors is a multistep enzymatic process consisting of nucleolytic size reducing reactions and of nucleotide modifications. |
| TAIR8_miRNA | microRNA | MicroRNAs are regulatory RNAs with a mature length of ~21-nucleotides that are processed from hairpin precursors by Dicer-like enzymes. MicroRNAs can negatively regulate gene expression by attenuating translation or by directing mRNA cleavage. For an example, see gene model AT3G04765.1 |
| TAIR8_ncRNA | non-coding RNA | A transcribed gene about which little is known, including whether or not its transcribed RNA is translated into protein via the usual mechanism. For an example, see gene model AT3G06125.1 |
| TAIR8_snRNA | small nuclear RNA | Also known as snRNA. Small nuclear RNA (snRNA) is the name used to refer to a number of small RNA molecules found in the nucleus. These RNA molecules are important in a number of processes including RNA splicing (removal of the introns from hnRNA) and maintenance of the telomeres, or chromosome ends. They are always found associated with specific proteins and the complexes are referred to as small nuclear ribonucleoproteins (SNRNP) or sometimes as snurps. |
| TAIR8_snoRNA | Small nuclear RNAs | Small nuclear RNAs (snoRNA) that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P. |
| TAIR8_rRNA | ribosomal rna | The transcribed product of ribosomal DNA, also known as rRNA. These rRNAs are part of the ribosome. |
Bioviz DAS2 Data Sets include genomic alignments of ESTs and cDNAs from GenBank. We used blat (default settings, with maximum intron size 35,000) to align the ESTs and cDNAs onto the TAIR8 genome. Only alignments in which the query sequence (EST or cDNA) aligned with 95% identify or better and where the alignment included 90% of the query sequence were kept.
Next, we sub-divided the alignments into two groups: The single map (sm) groups include sequences that aligned to one unique location in the genome. The multiple map groups (mm) include sequences that map onto more than one location in the genome. The latter group is useful mainly for visualizing highly-similar, duplicate regions in the genome.
| Data Set | Description |
|---|---|
| cDNA (single map) | Genome alignments for cDNAs from Genbank, obtained in fasta format from the Plant Genome Database ftp site in June, 2009. The file was time-stamped April 22, 2009. Each sequence in this data set aligned to the genome exactly according to the criteria described above. |
| cDNA (multiple map) | The same as cDNA (single map) described above, except that the cDNAs aligned more than once to the genome according to the criteria described above. |
| EST (single map) | Genome alignments for Arabidopsis ESTs from Genbank dbEST database aligned to the genome using the procedure described above. The data were from The ESTs data set included approximately 1.5 million ESTs and was obtained from Genbank's dbEST in November, 2008. Each sequence aligned just once under criteria described above. |
| EST (spliced, single map) | The subset of the EST (single map) alignments that included putative introns, e.g., gaps in the query greater than or equal to 30 bases. |
| EST (multiple map) | The same as the EST (single map) data set described above, except that each EST in this data set aligned more than once under the stringency criteria described above. |
Arabidopsis thaliana (Genome Version: A_thaliana_Jan_2004)
Bioviz Quickload Data Sets include gene annotations from the TAIR7 set. These include gene models for protein coding genes (TAIR7_protein_coding_gene data set) along with several other smaller data sets that include models for non-protein-coding genes, including micro-RNA (TAIR7_mirna), pre-tRNA (TAIR7_pre-trna), and other genes where the functional product is an RNA molecule and not a protein.
| Data Set | Source | Description (Adapted from this TAIR Help Page) |
|---|---|---|
| TAIR7_protein_coding_gene | protein coding | A gene model whose product is a transcript which is subsequently translated into a protein. |
| TAIR7_mirna | microRNA | MicroRNAs are regulatory RNAs with a mature length of ~21-nucleotides that are processed from hairpin precursors by Dicer-like enzymes. MicroRNAs can negatively regulate gene expression by attenuating translation or by directing mRNA cleavage. For an example, see gene model AT3G04765.1 |
| TAIR7_rrna | ribosomal rna | The transcribed product of ribosomal DNA, also known as rRNA. These rRNA's are part of the ribosome. |
| TAIR7_pre-trna | pre trna | A gene model in which the primary product of transcription codes for transfer RNAs (t-RNA). The pre-tRNA of prokaryotes and eukaryotes has extra nucleotides at the 5' and 3' extremities and in some eukaryotic pre-tRNAs introns are also present. Maturation of tRNA precursors is a multistep enzymatic process consisting of nucleolytic size reducing reactions and of nucleotide modifications. |
| TAIR7_other_rna | non-coding RNA | A transcibed gene about which little is known, including whether or not its transcribed RNA is translated into protein via the usual mechanism. For an example, see gene model AT3G06125.1 |
| TAIR7_snorna | Small nuclear RNAs | Small nuclear RNAs (snoRNA) that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P. |
| TAIR7_pseudogene | pseudogene | A gene model that represents a sequence of DNA that is very similar to a normal gene but that has been altered slightly so it is not expressed. Such genes were probably once functional but over time acquired one or more mutations that rendered them incapable of producing a protein product. For an example, see gene model AT1G06370.1 which probably once encoded a glycolipid alpha-mannosyltransferase enzyme. |
| TAIR7_snrna | small nuclear RNA | Also known as snRNA. Small nuclear RNA (snRNA) is the name used to refer to a number of small RNA molecules found in the nucleus. These RNA molecules are important in a number of processes including RNA splicing (removal of the introns from hnRNA) and maintenance of the telomeres, or chromosome ends. They are always found associated with specific proteins and the complexes are referred to as small nuclear ribonucleoproteins (SNRNP) or sometimes as snurps. |
Bioviz DAS2 Data Sets include genomic alignments of ESTs and cDNAs that we downloaded from TAIR and re-formatted for our server. We also sub-divided the data into two data set types: ESTs or cDNAs that mapped to multiple (mm) or just one (sm) locations in the genome. For details, see the table below:
| Data Set | Description |
|---|---|
| cDNA (multiple map) | cDNAs from GenBank aligned to the genome by TAIR and which align to more than one location. The original data file is from the TAIR ftp site. |
| cDNA (single map) | cDNAs from Genbank aligned to the genome by TAIR and which align to a single location in the genome. The original data file is from the TAIR ftp site. |
| EST (multiple map) | ESTs from Genbank dbEST database aligned to the genome by TAIR and which align to more than one location in the genome. The original data file is from the TAIR ftp site. |
| EST (single map) | ESTs from Genbank dbEST aligned to the genome by TAIR and which align to one location in the genome. The original data file is from the TAIR ftp site. |