Schema for D. mel Transcripts - BLAT Alignment of D. melanogaster Transcripts
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Database: DyakCAF1 Primary Table: DmelTranscriptsBLAT Row Count: 32,442   Data last updated: 2024-01-05
field | example | SQL type | info |
chrom | chr2L | varchar(255) | values |
chromStart | 8435 | int(10) unsigned | range |
chromEnd | 16146 | int(10) unsigned | range |
name | l(2)gl-RB | varchar(255) | values |
score | 844 | int(10) unsigned | range |
strand | - | char(1) | values |
thickStart | 8654 | int(10) unsigned | range |
thickEnd | 14685 | int(10) unsigned | range |
reserved | 0 | int(10) unsigned | range |
blockCount | 12 | int(11) | range |
blockSizes | 42,119,109,443,641,4,104,11... | longblob | |
chromStarts | 0,219,401,844,1349,2013,226... | longblob | |
id | FBtr0078166 | varchar(255) | values |
description | FBgn0002121 | 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 | 8435 | 16146 | l(2)gl-RB | 844 | - | 8654 | 14685 | 0 | 12 | 42,119,109,443,641,4,104,1194,776,93,20,30 | 0,219,401,844,1349,2013,2260,2421,3673,6195,7660,7681 | FBtr0078166 | FBgn0002121 |
chr2L | 8435 | 15922 | l(2)gl-RF | 842 | - | 8654 | 12823 | 0 | 11 | 42,119,109,443,641,4,104,1194,776,93,42 | 0,219,401,844,1349,2013,2260,2421,3673,6195,7445 | FBtr0078169 | FBgn0002121 |
chr2L | 8435 | 16146 | l(2)gl-RD | 842 | - | 8654 | 12823 | 0 | 13 | 42,119,109,443,641,4,104,1194,776,93,42,20,30 | 0,219,401,844,1349,2013,2260,2421,3673,6195,7445,7660,7681 | FBtr0078167 | FBgn0002121 |
chr2L | 8435 | 16146 | l(2)gl-RE | 842 | - | 8654 | 12823 | 0 | 13 | 42,119,109,443,641,4,104,1194,776,93,42,20,30 | 0,219,401,844,1349,2013,2260,2421,3673,6195,7445,7660,7681 | FBtr0078168 | FBgn0002121 |
chr2L | 8435 | 16146 | l(2)gl-RC | 842 | - | 8654 | 14685 | 0 | 14 | 42,119,109,443,641,4,104,1194,776,113,11,42,20,30 | 0,219,401,844,1349,2013,2260,2421,3673,6164,6308,7445,7660,7681 | FBtr0078170 | FBgn0002121 |
chr2L | 8435 | 16146 | l(2)gl-RA | 842 | - | 8654 | 14685 | 0 | 15 | 42,119,109,443,641,4,104,1194,776,113,42,67,42,20,30 | 0,219,401,844,1349,2013,2260,2421,3673,6164,7173,7270,7445,7660,7681 | FBtr0078171 | FBgn0002121 |
chr2L | 8435 | 16146 | l(2)gl-RG | 846 | - | 8654 | 14685 | 0 | 12 | 42,119,109,443,641,4,104,1194,776,113,20,30 | 0,219,401,844,1349,2013,2260,2421,3673,6164,7660,7681 | FBtr0306589 | FBgn0002121 |
chr2L | 8435 | 16146 | l(2)gl-RH | 838 | - | 8654 | 14685 | 0 | 13 | 42,119,109,443,641,4,104,1194,776,113,11,104,30 | 0,219,401,844,1349,2013,2260,2421,3673,6164,6308,7576,7681 | FBtr0306590 | FBgn0002121 |
chr2L | 8435 | 16146 | l(2)gl-RI | 842 | - | 8654 | 14685 | 0 | 13 | 42,119,109,443,641,4,104,1194,776,113,42,20,30 | 0,219,401,844,1349,2013,2260,2421,3673,6164,7445,7660,7681 | FBtr0306591 | FBgn0002121 |
chr2L | 8435 | 16146 | l(2)gl-RJ | 840 | - | 8654 | 14685 | 0 | 16 | 42,119,109,443,641,4,104,1194,776,113,11,42,67,42,20,30 | 0,219,401,844,1349,2013,2260,2421,3673,6164,6277,7173,7270,7445,7660,7681 | FBtr0306592 | FBgn0002121 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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D. mel Transcripts (DmelTranscriptsBLAT) Track Description
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Description
D. melanogaster transcripts annotated by FlyBase were aligned against the
D. yakuba genome assembly using a translated BLAT search. The thicker boxes denote
the coding regions within the transcripts and the thinner boxes denote the untranslated regions.
Methods
D. melanogaster transcripts were mapped against the D. yakuba
genome assembly using BLAT with the following parameters:
-q=rnax -t=dnax -mask=lower
The transcript alignments are analyzed by pslReps to identify the best alignments within the genome assembly that have a minimum alignment ratio of 0.25 (-minAli=0.25 ). The alignments are then filtered by pslCDnaFilter using the following parameters:
-minId=0.35 -minCover=0.15 -localNearBest=0.010 -minQSize=20
-ignoreIntrons -repsAsMatch -ignoreNs -bestOverlap
References
Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.
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