Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DhydGB1 Primary Table: cds_mapping Row Count: 65,421 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| chrom | NWQH01000001 | varchar(255) | values |
| chromStart | 24592 | int(10) unsigned | range |
| chromEnd | 24766 | int(10) unsigned | range |
| name | Adar:4_2172_0 | varchar(255) | values |
| score | 120 | int(10) unsigned | range |
| strand | + | char(1) | values |
| thickStart | 24592 | int(10) unsigned | range |
| thickEnd | 24766 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 11 | int(11) | range |
| blockSizes | 45,3,27,3,12,21,6,21,6,9,6, | longblob | |
| chromStarts | 0,45,51,81,84,99,126,132,15... | longblob | |
| id | Adar:4_2172_0 | varchar(255) | values |
| description | | longblob | |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | id | description |
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| NWQH01000001 | 24592 | 24766 | Adar:4_2172_0 | 120 | + | 24592 | 24766 | 0 | 11 | 45,3,27,3,12,21,6,21,6,9,6, | 0,45,51,81,84,99,126,132,153,159,168, | Adar:4_2172_0 | E-value: 5.5e-10Reading frame: +2Bit score: 59Percent identity: 5 ... |
| NWQH01000001 | 25280 | 25361 | Adar:6_2172_0 | 408 | + | 25280 | 25361 | 0 | 1 | 81, | 0, | Adar:6_2172_0 | E-value: 7.2e-08Reading frame: +3Bit score: 52Percent identity: 7 ... |
| NWQH01000001 | 25304 | 25361 | Adar:7_2172_0 | 686 | + | 25304 | 25361 | 0 | 1 | 57, | 0, | Adar:7_2172_0 | E-value: 2.6e-06Reading frame: +3Bit score: 47Percent identity: 8 ... |
| NWQH01000001 | 25490 | 25634 | Adar:8_2172_2 | 876 | + | 25490 | 25634 | 0 | 1 | 144, | 0, | Adar:8_2172_2 | E-value: 2.1e-28Reading frame: +3Bit score: 121Percent identity: ... |
| NWQH01000001 | 26820 | 26988 | Adar:11_2172_0 | 1000 | + | 26820 | 26988 | 0 | 1 | 168, | 0, | Adar:11_2172_0 | E-value: 6.9e-37Reading frame: +1Bit score: 149Percent identity: ... |
| NWQH01000001 | 26820 | 27117 | Adar:10_2172_0 | 742 | + | 26820 | 27117 | 0 | 3 | 216,48,15, | 0,219,282, | Adar:10_2172_0 | E-value: 1.7e-50Reading frame: +1Bit score: 194Percent identity: ... |
| NWQH01000001 | 26820 | 27126 | Adar:9_2172_0 | 750 | + | 26820 | 27126 | 0 | 3 | 216,48,24, | 0,219,282, | Adar:9_2172_0 | E-value: 5.9e-53Reading frame: +1Bit score: 202Percent identity: ... |
| NWQH01000001 | 27810 | 27987 | Adar:12_2172_2 | 832 | + | 27810 | 27987 | 0 | 1 | 177, | 0, | Adar:12_2172_2 | E-value: 8.9e-38Reading frame: +1Bit score: 152Percent identity: ... |
| NWQH01000001 | 28047 | 28326 | Adar:13_2172_2 | 894 | + | 28047 | 28326 | 0 | 1 | 279, | 0, | Adar:13_2172_2 | E-value: 2.4e-63Reading frame: +1Bit score: 237Percent identity: ... |
| NWQH01000001 | 28584 | 28734 | Adar:15_2172_0 | 1000 | + | 28584 | 28734 | 0 | 1 | 150, | 0, | Adar:15_2172_0 | E-value: 1.2e-33Reading frame: +1Bit score: 138Percent identity: ... |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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CDS Mapping (cds_mapping) Track Description
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Description
This track shows the tblastn alignment of the coding exons of D. melanogaster genes against
the D. hydei genome. The coding exon sequences were obtained from
FlyBase.
The tblastn search was performed using the following parameters:
-e=1e-2 -topComboN=1 -links -hspsepSmax=10000 -hspsepQmax=1000 -matrix=PAM40 -Q=7 -R=2
References
St Pierre SE, Ponting L, Stefancsik R, McQuilton P; FlyBase Consortium.
FlyBase 102 — advanced approaches to interrogating FlyBase.
Nucleic Acids Res. 2014 Jan;42(Database issue):D780-8
Gish, W. WU BLAST 2.0. (1996-2006)
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