Genome Annotations¶
Annotation sources¶
PATRIC provides two basic annotation sources, RefSeq, and PATRIC. RefSeq sequences from NCBI, have each been annotated by the submitting researcher using methodologies of their choice. PATRIC re-annotates all genomes using RAST tool kit (RASTtk) to provide annotation consistency across a wide variety of genomes. The original RefSeq annotations have been retained and are still available for comparison purposes.
Genomes that are in more than 500 contigs are not annotated by RAST. Nor are plasmid-only genomes. There is approximately a two-month interval between when sequences are submitted to RefSeq and re-annotation/integration with PATRIC, thus there may be a significant difference in the number of genomes at NCBI and at PATRIC.
Annotated Features¶
Currently, PATRIC supports the following genomic feature types:
-10_signal
-35_signal
5’UTR
attenuator
CDS
conflict
enhancer
exon
gene
intron
LTR
mat_peptide
misc_binding
misc_difference
misc_feature
misc_recomb
misc_RNA
misc_signal
misc_structure
mRNA
ncRNA
old_sequence
prim_transcript
primer_bind
promoter
protein_bind
pseudogene
pseudogenic_region
RBS
region
rep_origin
repeat_region
repeat_unit
ribosome_entry_site
rRNA
sig_peptide
source
stem_loop
terminator
tmRNA
transcript
tRNA
unsure
variation