Specialized Annotation - General
PlasmidFinder 2
PlasmidFinder 2
- identifies plasmids in total or partial sequenced isolates of
bacteria. The method uses BLAST for identification of replicons of
plasmids belonging to the major incompatibility (Inc) groups of
Enterobacteriaceae. As input, the method can use both pre-assembled,
complete or partial genomes, and short sequence reads from four different
sequencing platforms. See also
pMLST 2.0
(Reference: Carattoli A et al. 2014. Antimicrob.
Agents Chemother. 58: 3895-903)
HostPhinder 1.1
HostPhinder 1.1 (Danish Technical University)- identifies the bacterial host of a query phage genome based on its genomic similarity to a database of phage genomes with known host.
SpeciesFinder 2.0
SpeciesFinder 2.0 (Danish Technical University) - predicts the species of bacteria from pre-assembled, complete or partial genomes, and short sequence reads. The prediction is based on the 16S rRNA gene.
CSI Phylogeny 1.4
CSI Phylogeny 1.4
(Call SNPs & Infer Phylogeny; Danish Technical University) - calls SNPs,
filters the SNPs, does site validation and infers a phylogeny based on
the concatenated alignment of the high quality* SNPs.
(Reference: Kaas, R.S. et al. PLoS ONE 2014; 9:
e104984.)
KmerFinder 3.2
KmerFinder 3.2
(Danish Technical University) – predicts the species of bacteria from
pre-assembled, complete or partial genomes, and short sequence reads. The
prediction is based on the number of co-occurring k-mers (substrings of k
nucleotides in DNA sequence data, in this case 16-mers) between the
genomes of reference bacteria in a database and the genome provided by
the user.
(Reference: Hasman H et al. 2013. J Clin Microbiol.
52:139-146)
VIOLIN
VIOLIN
- Vaccine Investigation and Online Information Network - allows easy
curation, comparison and analysis of vaccine-related research data across
various human pathogens VIOLIN is expected to become a centralized source
of vaccine information and to provide investigators in basic and clinical
sciences with curated data and bioinformatics tools for vaccine research
and development. VBLAST: Customized BLAST Search for Vaccine Research
allows various search strategies against against 77 genomes of 34
pathogens.
(Reference: He, Y. et al. 2014. Nucleic Acids Res.
42 (Database issue):D1124-32).
MLST 2.0
MLST 2.0
(MultiLocus Sequence Typing) - currently only works with assembled
genomes and contigs
(Reference: Larsen MV et al. 2012. J. Clin. Micobiol.
50: 1355-1361).
AutoMLST2
AutoMLST2 -
they have enhanced AutoMLST to leverage newer reference databases and computational tools. AutoMLST2 integrates the Genome
Taxonomy Database, extends support to archaeal genomes, and improves analytical flexibility. Key improvements include more
customizable processing modes (e.g. Rapid ANI), containerization to prevent queue accumulations, and parallel computing for
large-scale studies.
(Reference: Pourmohsenin B et al. 2025. Nucleic Acids Research 53(W1): W45 - W50).
BacWGSTdb
BacWGSTdb
- incorporates extensive resources for bacterial genome sequencing data
and the corresponding metadata, combined with specialized bioinformatics
tools that enable the systematic characterization of the bacterial
isolates recovered from infections: (i) the integration of the core
genome multi-locus sequence typing (cgMLST) approach; (ii) the addition
of a multiple genome analysis module that can process dozens of user
uploaded sequences in a batch mode; (iii) a new source tracking module
for comparing plasmid sequences to those deposited in the public
databases; and (iv) the number of species encompassed in BacWGSTdb 2.0
has increased from 9 to 20.
(Reference: Feng Y et al (2021) Nucleic Acids
Research. 2016; 44(D1): D682-D687).
InBase
InBase,
The Intein Database and Registry (legacy hosted by Hideo Iwai lab)
Protein splicing is defined as the excision of an intervening protein
sequence (the INTEIN) from a protein precursor and the concomitant
ligation of the flanking protein fragments (the EXTEINS) to form a mature
extein host protein and the free intein (Perler 1994). Protein splicing
results in a native peptide bond between the ligated exteins. This is a
database site which permits BLAST analysis.
(Reference: Perler, F.B. 2002. Nucleic Acids Res.
30: 383-384).
Updated: February, 2026