Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DyakCAF1 Primary Table: cds_mapping Row Count: 63,758 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| chrom | chr2L | varchar(255) | values |
| chromStart | 8646 | int(10) unsigned | range |
| chromEnd | 8772 | int(10) unsigned | range |
| name | l(2)gl:11_348_1 | varchar(255) | values |
| score | 954 | int(10) unsigned | range |
| strand | - | char(1) | values |
| thickStart | 8646 | int(10) unsigned | range |
| thickEnd | 8772 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 1 | int(11) | range |
| blockSizes | 126, | longblob | |
| chromStarts | 0, | longblob | |
| id | l(2)gl:11_348_1 | 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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| chr2L | 8646 | 8772 | l(2)gl:11_348_1 | 954 | - | 8646 | 8772 | 0 | 1 | 126, | 0, | l(2)gl:11_348_1 | E-value: 5.6e-25Reading frame: -1Bit score: 109Percent identity: ... |
| chr2L | 8838 | 8943 | l(2)gl:9_348_2 | 886 | - | 8838 | 8943 | 0 | 1 | 105, | 0, | l(2)gl:9_348_2 | E-value: 1.6e-19Reading frame: -1Bit score: 91Percent identity: 9 ... |
| chr2L | 9280 | 9721 | l(2)gl:8_348_1 | 660 | - | 9280 | 9721 | 0 | 1 | 441, | 0, | l(2)gl:8_348_1 | E-value: 1.8e-86Reading frame: -3Bit score: 314Percent identity: ... |
| chr2L | 9786 | 10425 | l(2)gl:7_348_2 | 908 | - | 9786 | 10425 | 0 | 1 | 639, | 0, | l(2)gl:7_348_2 | E-value: 8.7e-155Reading frame: -1Bit score: 541Percent identity: ... |
| chr2L | 10694 | 10799 | l(2)gl:6_348_0 | 1000 | - | 10694 | 10799 | 0 | 1 | 105, | 0, | l(2)gl:6_348_0 | E-value: 9.6e-22Reading frame: -2Bit score: 99Percent identity: 1 ... |
| chr2L | 10856 | 12047 | l(2)gl:5_348_1 | 930 | - | 10856 | 12047 | 0 | 1 | 1191, | 0, | l(2)gl:5_348_1 | E-value: 4.1e-302Reading frame: -2Bit score: 1030Percent identity ... |
| chr2L | 12108 | 12822 | l(2)gl:3_348_0 | 908 | - | 12108 | 12822 | 0 | 1 | 714, | 0, | l(2)gl:3_348_0 | E-value: 5.2e-180Reading frame: -1Bit score: 624Percent identity: ... |
| chr2L | 12108 | 12885 | l(2)gl:4_348_0 | 916 | - | 12108 | 12885 | 0 | 1 | 777, | 0, | l(2)gl:4_348_0 | E-value: 4.3e-197Reading frame: -1Bit score: 681Percent identity: ... |
| chr2L | 14600 | 14684 | l(2)gl:2_348_0 | 858 | - | 14600 | 14684 | 0 | 1 | 84, | 0, | l(2)gl:2_348_0 | E-value: 4.8e-15Reading frame: -2Bit score: 76Percent identity: 9 ... |
| chr2L | 14630 | 14684 | l(2)gl:1_348_0 | 890 | - | 14630 | 14684 | 0 | 1 | 54, | 0, | l(2)gl:1_348_0 | E-value: 1.4e-07Reading frame: -2Bit score: 52Percent identity: 9 ... |
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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. yakuba 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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