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Genome annotation script |
3. Scripts |
genome annotation SwissProt CDS.sh is a bash script that annotates the coding sequences (CDS) in a given genome assembly.
It uses BLAST and MGKit, which are included in the bioinfo-notebook conda environment.
genome_annotation_SwissProt_CDS.sh [-h|--help] [-d|--demo] [-i|--input]
[-l|--log -p|--processors n -e|--email]
A script to annotate proteins in a genome assembly, using BLASTx with
UniProtKB/Swiss-Prot.
When run with the arugment '-d' or '--demo' this script...
1. Downloads a Saccharomyces cerevisiae S288C genome assembly, and
the UniProtKB/Swiss-Prot amino acid sequences.
2. Creates a BLAST database from the downloaded Swiss-Prot sequences,
and searches the S. cerevisiae genome against it using BLASTx with an
E-value threshold of 1e-100.
3. Filters the BLASTx results, removing results with less than 90%
identity.
4. Creates a genome annotation GFF file from these BLASTx results.
5. Adds information to the genome annotation from UniProt (protein
names, KeGG ortholog information, EC numbers, etc.)
The end result ('S_cere.gff') is an annotation of the coding sequences (CDS)
in the S. cerevisiae genome that are described in UniProtKB/Swiss-Prot.
This script can also be run with the argument '-i' or '--input', which is used
to specify a FASTA nucleotide file (.fasta or .fna) to annotate, instead of
the demo sequence. The end result is also an annotation of the CDS in the input
sequence based on UniProtKB/Swiss-Prot, called '<input>.gff'.
This script should be called from the 'bioinfo-notebook/' directory.The
programs required for this script are in the 'bioinfo-notebook' conda
environment (bioinfo-notebook/envs/bioinfo-notebook.yml or
bioinfo-notebook/envs/bioinfo-notebook.txt).
If the input file is not in the 'bioinfo-notebook/data/' directory, the full
file path should be given.
arguments:
-h | --help show this help text and exit
-i | --input name of input FASTA nucleotide file to annotate
-d | --demo run the script with demonstration inputs
optional arguments:
-l | --log redirect terminal output to a log file
-p | --processors set the number (n) of processors to use
(default: 1)
-e | --email contact email for UniProt queries