Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DanaCAF1 Primary Table: cds_mapping Row Count: 63,128 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| chrom | scaffold_0 | varchar(255) | values |
| chromStart | 157 | int(10) unsigned | range |
| chromEnd | 334 | int(10) unsigned | range |
| name | CG17121:3_8877_0 | varchar(255) | values |
| score | 1000 | int(10) unsigned | range |
| strand | + | char(1) | values |
| thickStart | 157 | int(10) unsigned | range |
| thickEnd | 334 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 1 | int(11) | range |
| blockSizes | 177, | longblob | |
| chromStarts | 0, | longblob | |
| id | CG17121:3_8877_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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| scaffold_0 | 157 | 334 | CG17121:3_8877_0 | 1000 | + | 157 | 334 | 0 | 1 | 177, | 0, | CG17121:3_8877_0 | E-value: 4.2e-41Reading frame: +2Bit score: 162Percent identity: ... |
| scaffold_10042 | 558 | 750 | CG16952:3_3475_0 | 366 | - | 558 | 750 | 0 | 2 | 48,141, | 0,51, | CG16952:3_3475_0 | E-value: 5.1e-26Reading frame: -3Bit score: 113Percent identity: ... |
| scaffold_10042 | 609 | 711 | CG16952:5_3475_0 | 648 | - | 609 | 711 | 0 | 1 | 102, | 0, | CG16952:5_3475_0 | E-value: 7.8e-15Reading frame: -3Bit score: 76Percent identity: 8 ... |
| scaffold_10042 | 609 | 750 | CG16952:4_3475_0 | 532 | - | 609 | 750 | 0 | 1 | 141, | 0, | CG16952:4_3475_0 | E-value: 1.2e-21Reading frame: -3Bit score: 99Percent identity: 7 ... |
| scaffold_10061 | 3555 | 3600 | CG6340:4_3433_0 | 734 | - | 3555 | 3600 | 0 | 1 | 45, | 0, | CG6340:4_3433_0 | E-value: 0.0066Reading frame: -3Bit score: 38Percent identity: 86 ... |
| scaffold_10103 | 470 | 662 | CG16952:3_3475_0 | 366 | - | 470 | 662 | 0 | 2 | 48,141, | 0,51, | CG16952:3_3475_0 | E-value: 5.2e-26Reading frame: -1Bit score: 113Percent identity: ... |
| scaffold_10103 | 521 | 623 | CG16952:5_3475_0 | 648 | - | 521 | 623 | 0 | 1 | 102, | 0, | CG16952:5_3475_0 | E-value: 7.9e-15Reading frame: -1Bit score: 76Percent identity: 8 ... |
| scaffold_10103 | 521 | 662 | CG16952:4_3475_0 | 532 | - | 521 | 662 | 0 | 1 | 141, | 0, | CG16952:4_3475_0 | E-value: 1.2e-21Reading frame: -1Bit score: 99Percent identity: 7 ... |
| scaffold_10103 | 3246 | 3489 | CG16952:1_3475_0 | 656 | - | 3246 | 3489 | 0 | 1 | 243, | 0, | CG16952:1_3475_0 | E-value: 2.1e-51Reading frame: -3Bit score: 176Percent identity: ... |
| scaffold_10103 | 3546 | 3648 | CG16952:1_3475_0 | 132 | - | 3546 | 3648 | 0 | 3 | 15,42,42, | 0,18,60, | CG16952:1_3475_0 | E-value: 2.1e-51Reading frame: -3Bit score: 37Percent identity: 5 ... |
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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. ananassae 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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