Eukaryotic gene prediction on a bacterial genome

Euk-Ecoli.md

The goal is to check whether abinitio gene finders with eukaryotic parameters will predict genes with "real" introns in bacterial genomes.

Download E. coli from NCBI

http://www.ncbi.nlm.nih.gov/nuccore/296142109

Rename Header to >E_coli

Run CEGMA

cegma -g E_coli_BL21.fa -T 8 -o e_coli

Completeness report

#      Statistics of the completeness of the genome based on 248 CEGs      #

              #Prots  %Completeness  -  #Total  Average  %Ortho

  Complete       34       13.71      -    42     1.24     23.53

   Group 1        7       10.61      -     9     1.29     28.57
   Group 2        7       12.50      -     8     1.14     14.29
   Group 3        9       14.75      -    11     1.22     22.22
   Group 4       11       16.92      -    14     1.27     27.27

   Partial       35       14.11      -    45     1.29     28.57

   Group 1        8       12.12      -    12     1.50     50.00
   Group 2        7       12.50      -     8     1.14     14.29
   Group 3        9       14.75      -    11     1.22     22.22
   Group 4       11       16.92      -    14     1.27     27.27

Run GeneMark with Eukaryotic parameters

gmes_petap.pl --ES --cores 8 --sequence E_coli_BL21.fa

GeneMark predicts 2034 genes, 797 of which have introns.

Extract splice sites

Convert genemark gtf to gff3 (script from MAKER)

genemark_gtf2gff3 genemark.gtf > genemark.gff3

Add introns to gff (GenomeTools)

gt gff3 -addintrons yes -retainids yes genemark.gff3 > genemark_introns.gff3

Extract splice introns regions

grep intron genemark_introns.gff3 | cut -f 4,5,7 | \
perl -ane '
    if ($F[2] eq "+") {
        printf STDOUT "E_coli\t%d\t%d\n",$F[0]-20,$F[0]+20; printf STDERR "E_coli\t%d\t%d\n",$F[1]-20,$F[1]+20; 
    } 
    else {
        printf STDERR "E_coli\t%d\t%d\n",$F[0]+20,$F[0]-20;printf STDOUT "E_coli\t%d\t%d\n",$F[1]+20,$F[1]-20;
    }' > 5_prime_splice.txt 2>3_prime_splice.txt

Extract splice intron sequences (script from BlaxterLab github)

fastaqual_select.pl -f E_coli_BL21.fa -i 5_prime_splice.txt -int > 5_prime_splice.txt.fna
fastaqual_select.pl -f E_coli_BL21.fa -i 3_prime_splice.txt -int > 3_prime_splice.txt.fna

Visualise Results

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