Data Wrangling - Gene ID Extraction from P.generosa Genome GFF Using Methylation Machinery Gene IDs

2021
Miscellaneous
Author

Sam White

Published

February 26, 2021

Per this GitHub issue, Steven provided a list of methylation-related gene names and wanted to extract the corresponding Panopea generosa ([Pacific geoduck (Panopea generosa)](http://en.wikipedia.org/wiki/Geoduck)) gene ID from our P.generosa genome, along with corresponding BLAST e-values.

Everything is documented in the Jupyter Notebook linked below.

Here’s the list of gene IDs of interest:

dnmt1
dnmt3a
dnmt3b
dnmt3l
mbd1
mbd2
mbd3
mbd4
mbd5
mbd6
mecp2
Baz2a
Baz2b
UHRF1
UHRF2
Kaiso
zbtb4
zbtb38b
zfp57
klf4
egr1
wt1
ctcf
tet1
tet2
tet3

The gist of the process was like this:

  1. grep gene IDs in Panopea-generosa-vv0.74.a4.gene.gff3

  2. Use resulting P.generosa genome IDs to grep BLASTp and DIAMOND BLASTx tables (Panopea-generosa-vv0.74.a4.5d951a9b74287-blast_functional.tab and Panopea-generosa-vv0.74.a4.5d951bcf45b4b-diamond_functional.tab) to extract e-values.

Jupyter Notebook (GitHub):

Jupyter Notebook (NBviewer):

Jupyter Notebook:

RESULTS

Here’s the final table:

Gene_ID gene_name BLASTp_evalue DIAMOND_evalue
PGEN_.00g104080 Baz2b 1.05E-98 5.40E-102
PGEN_.00g104170 Baz2b 3.09E-96 1.20E-109
PGEN_.00g116950 mbd5 6.40E-21 2.80E-20
PGEN_.00g186870 ctcf 1.25E-116
PGEN_.00g192900 UHRF1 2.32E-19
PGEN_.00g202750 mbd2 9.46E-82 2.60E-63
PGEN_.00g209890 mbd2 4.37E-19 9.20E-09
PGEN_.00g209900 mbd4 3.14E-32 8.00E-29
PGEN_.00g243700 egr1 6.24E-58 2.20E-23
PGEN_.00g249090 egr1 4.19E-18 2.60E-06
PGEN_.00g283000 dnmt1 5.03E-10 8.20E-28
PGEN_.00g283010 dnmt1 0 7.30E-224