• AnEugene000

Summary

This analysis runs the EuGene gene prediction on BAC sequences using extrinsic data and ab-initio predictions from other gene finders, and produces the prediction as an GFF3 output, and the protein, cds, & cDNA sequences of each predicted genes in separate FASTA files.

Input

• BAC sequences from seq
  mapped EST data from transcripts_tomato, transcripts_sol
  BlastX and TBlastX output converted into a EuGene-specific format
  repeatmasking data from repeats
  ab-initio gene predictions from GeneID, AUGUSTUS, GeneMark, & GlimmerHMM
  

BlastX

• Splits the query sequences into sequences of 10000nt, and runs BlastX against Arabidopsis proteins, and Swissprot_uniprot
  blastall -p blastx -d $blastDB -i tempseq.tfa -g F -v 1000 -b 1000 -e 0.1 -L $x,$y
  

TBlastX

• Runs decypher-TBlastX against finished dicot genomes (Arabidopsis & Poplar) with a cutoff of 0.0001, max scores and max alignments of 5000
  dc_template_rt -template tera-tblastx.txt -query $fasta -targ dicot_genomes
  

Protein Mapping

• Maps Solanaceae proteins in NCBI with GenomeThreader. A very high weight is assigned to the mapped proteins via AnnotaStruct of Eugene
  gth -genomic ${i}.fasta -protein Solanaceae_Proteins_NCBI.tfa -species arabidopsis -mincoverage 0.95 -minalignmentscore 0.9 -force -o ${i}.gth.out
  

EuGene

• (eugene -A eugene.par -p g -d -b01 -B -E -r -s $IN ) >& ${IN}.log
  

Output

• Gene predictions, protein, cds, & cDNA sequences of the predictions

Filenames

• annotations:gff3 (ID.VER.eugene.annotations.itagXXX.batchXXX.vX.gff3)
  proteins:gff3 (ID.VER.eugene.proteins.itagXXX.batchXXX.vX.fasta)
  cds:gff3 (ID.VER.eugene.cds.itagXXX.batchXXX.vX.fasta)
  cdna:gff3 (ID.VER.eugene.cdna.itagXXX.batchXXX.vX.fasta)
  

Gene Descriptions

The gene name and description line basically follows the Guidelines Doc, although the functional description is not included.
We have also modified the 'Evidence Code' by expanding the single letter code used in Medicago into a multiple letter tag and adding some extra information. This 'structural tag' is currently being discussed within our group, and changes may occur in the future.
For the moment, the tag looks like - XXF()H()E()I()L(), e.g. 08F0H1E0IEGL1;