Schema for GeMoMa Genes - GeMoMa Gene Predictions
  Database: DereCAF1    Primary Table: GeMoMa    Row Count: 13,211   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
name FBTR0091810_R4varchar(255) values
chrom scaffold_1121varchar(255) values
strand -char(1) values
txStart 48int(10) unsigned range
txEnd 438int(10) unsigned range
cdsStart 48int(10) unsigned range
cdsEnd 438int(10) unsigned range
exonCount 1int(10) unsigned range
exonStarts 48,longblob  
exonEnds 438,longblob  
score 0int(11) range
name2 gene_0varchar(255) values
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values
exonFrames 0,longblob  

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585FBTR0091810_R4scaffold_1121-4843848438148,438,0gene_0unkunk0,
585FBTR0082679_R6scaffold_1128+812181781218171812,1817,0gene_1unkunk0,
585FBTR0077470_R1scaffold_1247-2446012446011244,601,0gene_2unkunk0,
585FBTR0111241_R1scaffold_1361-152021801520218021520,1672,1615,2180,0gene_3unkunk1,0,
585FBTR0072634_R0scaffold_1383+354139643541396413541,3964,0gene_4unkunk0,
585FBTR0072634_R1scaffold_1383+666470876664708716664,7087,0gene_5unkunk0,
585FBTR0082086_R0scaffold_1388+601689686016896836016,6609,8701,6551,8426,8968,0gene_6unkunk0,1,0,
585FBTR0347010_R1scaffold_1399+235167123516714235,584,1041,1592,277,779,1535,1671,0gene_7unkunk0,0,0,2,
585FBTR0083367_R2scaffold_1408+283438182834381832834,2931,3421,2878,3363,3818,0gene_8unkunk0,2,2,
585FBTR0307509_R1scaffold_1425+269748682697486852697,2868,3118,3877,4830,2808,3028,3607,4774,4868,0gene_9unkunk0,0,1,1,1,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

GeMoMa Genes (GeMoMa) Track Description
 

Description

D. melanogaster protein sequences from FlyBase were aligned against each scaffold in the D. erecta (DereCAF1) assembly and the predicted gene models were constructed using GeMoMa.

Methods

D. melanogaster protein sequences were aligned against the D. erecta (DereCAF1) genome assembly using NCBI TBLASTN with the following parameters:

  -evalue 1e-5
  -max_intron_length 100000
  -matrix BLOSUM80
  -gapopen 13
  -gapextend 2
  -soft_masking true
  -db_soft_mask 30
  -best_hit_overhang 0.1
  -best_hit_score_edge 0.1

The TBLASTN results were used by GeMoMa to produce an initial set of gene predictions. The GeMoMa predictions are then filtered by the GAF module in GeMoMa to produce the final set of gene predictions.

References

Keilwagen J, Wenk M, Erickson JL, Schattat MH, Grau J, Hartung F. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 2016 May 19;44(9):e89.