For example, signaling motif, T cell or B cell binding site, hydrophobic region, and so on. For reverse vaccinology.
This is a great platform from JGI,
http://img.jgi.doe.gov/cgi-bin/w/main.cgi
For annotation:
I like Interpro http://www.ebi.ac.uk/interpro/ from EMBL-EBI
KAAS - KEGG Automatic Annotation Server
for ortholog assignment and pathway mapping
http://www.genome.jp/tools/kaas/
PFAM to study specific domains http://pfam.sanger.ac.uk/ although you can obtain domain assignation also by using Interpro.
I hope this help
RAST server are a good option, but you can try BASYS
http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/RapidAnnotationServer
http://basys.ca/basys/cgi/submit.pl
another option iss the genoscope page
https://www.genoscope.cns.fr/agc/microscope/about/services.php?
The B-cell epitopes can be predicted by the ANTIGENIC program in EMBOSS (http://bioinfo.hku.hk/EMBOSS/). Potential Th epitopes can be predicted by the ProPred HLA-DR binding peptide prediction program (http://www.imtech.res.in/cgibin/hlapred)
Glimmer then kegg to get started then PDB - then a group specific site
For T cell epitope prediction, I recommend IEDB (http://www.immuneepitope.org/) but also caution that any prediction tool will have a high rate of false-positives.
Hi, Dear Vincent
I have attached a paper plus a few websites i hope they can be useful.
Good Luck
http://exon.gatech.edu/metagenome/portalDB/
http://microbiome.osu.edu/
http://commonfund.nih.gov/hmp/databases.aspx
May I ask the questions more specifically? If I have 10 strains genome of a bacteria from NCBI. Firstly, I want to analyze to find a list of genes that are homologous in these strains. Secondly, I wonder to screen size below to 30-50 kDa and annotate their functions. What tools could I do? Thanks.
you can use Mauve to identify the core gene shared among these 10 starins
as for your second question, you can used a Perl script to extract all predicted protein from your bacterial genome (GenBank). and then predicted the protein size in batch module using ExPASy
I they are just strains, maybe a Reciporcal Blast Best Hit is another option. You can use OrthoMCL too, but is a little hard to install. For annotation, hmmer coul be an option if you don't have so much proteins or Blast2Go.
I have done by MBGD (microbial Genome database) and combined (Perl script) with MicroScope to resolve these problems, thank you all.
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