Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
|---|
| |
Database: DsimGB2 Primary Table: cds_mapping Row Count: 62,836 Data last updated: 2024-01-05
| field | example | SQL type | info |
|---|
| chrom | CM002910 | varchar(255) | values |
| chromStart | 5297 | int(10) unsigned | range |
| chromEnd | 5423 | int(10) unsigned | range |
| name | l(2)gl:11_348_1 | varchar(255) | values |
| score | 906 | int(10) unsigned | range |
| strand | - | char(1) | values |
| thickStart | 5297 | int(10) unsigned | range |
| thickEnd | 5423 | 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 | |
|
| |
|
|
|
Sample Rows
|
|---|
| |
| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | id | description |
|---|
| CM002910 | 5297 | 5423 | l(2)gl:11_348_1 | 906 | - | 5297 | 5423 | 0 | 1 | 126, | 0, | l(2)gl:11_348_1 | E-value: 9.2e-24Reading frame: -3Bit score: 105Percent identity: ... |
| CM002910 | 5489 | 5594 | l(2)gl:9_348_2 | 944 | - | 5489 | 5594 | 0 | 1 | 105, | 0, | l(2)gl:9_348_2 | E-value: 4.4e-20Reading frame: -3Bit score: 93Percent identity: 9 ... |
| CM002910 | 5859 | 6300 | l(2)gl:8_348_1 | 852 | - | 5859 | 6300 | 0 | 1 | 441, | 0, | l(2)gl:8_348_1 | E-value: 9.0e-100Reading frame: -2Bit score: 357Percent identity: ... |
| CM002910 | 6375 | 7014 | l(2)gl:7_348_2 | 926 | - | 6375 | 7014 | 0 | 1 | 639, | 0, | l(2)gl:7_348_2 | E-value: 8.2e-158Reading frame: -2Bit score: 550Percent identity: ... |
| CM002910 | 7582 | 7687 | l(2)gl:6_348_0 | 1000 | - | 7582 | 7687 | 0 | 1 | 105, | 0, | l(2)gl:6_348_0 | E-value: 7.2e-22Reading frame: -1Bit score: 99Percent identity: 1 ... |
| CM002910 | 7744 | 8935 | l(2)gl:5_348_1 | 966 | - | 7744 | 8935 | 0 | 1 | 1191, | 0, | l(2)gl:5_348_1 | E-value: 0.Reading frame: -1Bit score: 1047Percent identity: 98.2 ... |
| CM002910 | 8996 | 9710 | l(2)gl:3_348_0 | 942 | - | 8996 | 9710 | 0 | 1 | 714, | 0, | l(2)gl:3_348_0 | E-value: 3.7e-184Reading frame: -3Bit score: 638Percent identity: ... |
| CM002910 | 8996 | 9773 | l(2)gl:4_348_0 | 946 | - | 8996 | 9773 | 0 | 1 | 777, | 0, | l(2)gl:4_348_0 | E-value: 3.1e-201Reading frame: -3Bit score: 694Percent identity: ... |
| CM002910 | 11171 | 11255 | l(2)gl:2_348_0 | 930 | - | 11171 | 11255 | 0 | 1 | 84, | 0, | l(2)gl:2_348_0 | E-value: 1.3e-15Reading frame: -3Bit score: 78Percent identity: 9 ... |
| CM002910 | 11201 | 11255 | l(2)gl:1_348_0 | 1000 | - | 11201 | 11255 | 0 | 1 | 54, | 0, | l(2)gl:1_348_0 | E-value: 3.9e-08Reading frame: -3Bit score: 53Percent identity: 1 ... |
|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
| |
|
|
|
CDS Mapping (cds_mapping) Track Description
|
|---|
| |
Description
This track shows the tblastn alignment of the coding exons of D. melanogaster genes against
the D. simulans 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)
| |
|
|
|