GeMoMa Genes Track Settings

GeMoMa Gene Predictions with RNA-Seq (All Genes and Gene Prediction Tracks)

Display mode:

Color track by codons: Help on codon coloring

Show codon numbering:

Display data as a density graph:

Data last updated at UCSC: 2022-10-20

Description

This track shows the GeMoMa gene predictions based on D. kikkawai RNA-Seq data and sequence similarity to D. melanogaster protein sequences.

Methods

D. melanogaster protein sequences were aligned against the D. kikkawai (DkikHiC1) 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

Mapped RNA-Seq reads were analyzed by the ExtractRNAseqEvidence (ERE) tool in GeMoMa. The RNA-Seq read coverage and extracted splice junctions were used in conjunction with the TBLASTN results by GeMoMa to produce an initial set of gene predictions. These gene predictions are then filtered by the GAF module in GeMoMa to produce the final set of gene predictions.

References

Keilwagen J, Hartung F, Paulini M, Twardziok SO, Grau J. Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC Bioinformatics. 2018 May 30;19(1):189.