PSAT Home
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Explore Homologies
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User's Manual
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NCBI
For publication of results, please cite:
Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.
PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes. BMC Bioinformatics. 2008 Mar 26;9(1):170
Analysis Options
1. Select Reference and Comparison Genome(s):
Genomes last loaded from NCBI on 2010-01-25
Reference Genome
Comparison Genome(s)
Select a genus:
Bacillus
Brucella
Burkholderia
Coxiella
Escherichia
Francisella
Pseudomonas
Salmonella
Shigella
Vibrio
Yersinia
Select a species:
Selected reference genome:
Select a genus or
all genomes:
Acaryochloris
Acetobacter
Acholeplasma
Acidaminococcus
Acidimicrobium
Acidiphilium
Acidithiobacillus
Acidobacterium
Acidothermus
Acidovorax
Aciduliprofundum
Acinetobacter
Actinobacillus
Actinosynnema
Aeromonas
Aeropyrum
Aggregatibacter
Agrobacterium
Akkermansia
Alcanivorax
Alicyclobacillus
Aliivibrio
Alkalilimnicola
Alkaliphilus
Allochromatium
Alteromonas
Aminobacterium
Ammonifex
Anabaena
Anaerocellum
Anaerococcus
Anaeromyxobacter
Anaplasma
Anoxybacillus
Aquifex
Archaeoglobus
Arcobacter
Aromatoleum
Arthrobacter
Aster
Atopobium
Azoarcus
Azorhizobium
Azospirillum
Azotobacter
Bacillus
Bacteroides
Bartonella
Baumannia
Bdellovibrio
Beijerinckia
Beutenbergia
Bifidobacterium
Blattabacterium
Bordetella
Borrelia
Brachybacterium
Brachyspira
Bradyrhizobium
Brevibacillus
Brucella
Buchnera
Burkholderia
Caldicellulosiruptor
Caldivirga
Campylobacter
Candidatus
Capnocytophaga
Carboxydothermus
Catenulispora
Caulobacter
Cellulomonas
Cellvibrio
Chitinophaga
Chlamydia
Chlamydophila
Chlorobaculum
Chlorobium
Chloroflexus
Chloroherpeton
Chromobacterium
Chromohalobacter
Citrobacter
Clavibacter
Clostridiales
Clostridium
Colwellia
Comamonas
Conexibacter
Coprothermobacter
Coraliomargarita
Corynebacterium
Coxiella
Cronobacter
Cryptobacterium
Cupriavidus
Cyanobacteria
Cyanothece
Cytophaga
Dechloromonas
Deferribacter
Dehalococcoides
Deinococcus
Delftia
Denitrovibrio
Desulfatibacillum
Desulfitobacterium
Desulfobacterium
Desulfohalobium
Desulfomicrobium
Desulfotalea
Desulfotomaculum
Desulfovibrio
Desulfurococcus
Diaphorobacter
Dichelobacter
Dickeya
Dictyoglomus
Dinoroseobacter
Dyadobacter
Edwardsiella
Eggerthella
Ehrlichia
Elusimicrobium
Enterobacter
Enterococcus
Erwinia
Erythrobacter
Escherichia
Eubacterium
Exiguobacterium
Ferroglobus
Fervidobacterium
Fibrobacter
Finegoldia
Flavobacteriaceae
Flavobacterium
Francisella
Frankia
Fusobacterium
Gardnerella
Gemmatimonas
Geobacillus
Geobacter
Geodermatophilus
Gloeobacter
Gluconacetobacter
Gluconobacter
Gordonia
Gramella
Granulobacter
Haemophilus
Hahella
Haliangium
Haloarcula
Halobacterium
Haloferax
Halomicrobium
Haloquadratum
Halorhabdus
Halorhodospira
Halorubrum
Haloterrigena
Halothermothrix
Halothiobacillus
Helicobacter
Heliobacterium
Herminiimonas
Herpetosiphon
Hirschia
Hydrogenobacter
Hydrogenobaculum
Hyperthermus
Hyphomonas
Idiomarina
Ignicoccus
Jannaschia
Janthinobacterium
Jonesia
Kangiella
Kineococcus
Klebsiella
Kocuria
Kosmotoga
Kribbella
Kytococcus
Lactobacillus
Lactococcus
Laribacter
Lawsonia
Legionella
Leifsonia
Leptospira
Leptothrix
Leptotrichia
Leuconostoc
Listeria
Lysinibacillus
Macrococcus
Magnetococcus
Magnetospirillum
Mannheimia
Maricaulis
Marinobacter
Marinomonas
Meiothermus
Mesoplasma
Mesorhizobium
Metallosphaera
Methanobacterium
Methanobrevibacter
Methanocaldococcus
Methanocella
Methanococcoides
Methanococcus
Methanocorpusculum
Methanoculleus
Methanohalophilus
Methanopyrus
Methanosaeta
Methanosarcina
Methanosphaera
Methanospirillum
Methylacidiphilum
Methylibium
Methylobacillus
Methylobacterium
Methylocella
Methylococcus
Methylotenera
Methylovorus
Micrococcus
Microcystis
Moorella
Moraxella
Mycobacterium
Mycoplasma
Myxococcus
Nakamurella
Nanoarchaeum
Natranaerobius
Natrialba
Natronomonas
Nautilia
Neisseria
Neorickettsia
Nitratiruptor
Nitrobacter
Nitrosococcus
Nitrosomonas
Nitrosopumilus
Nitrosospira
Nocardia
Nocardioides
Nostoc
Novosphingobium
Oceanobacillus
Ochrobactrum
Oenococcus
Oligotropha
Onion
Opitutus
Orientia
Paenibacillus
Pantoea
Parabacteroides
Parachlamydia
Paracoccus
Parvibaculum
Pasteurella
Pectobacterium
Pediococcus
Pedobacter
Pelobacter
Pelodictyon
Pelotomaculum
Persephonella
Petrotoga
Phenylobacterium
Photobacterium
Photorhabdus
Picrophilus
Pirellula
Planctomyces
Polaromonas
Polynucleobacter
Porphyromonas
Prevotella
Prochlorococcus
Propionibacterium
Prosthecochloris
Proteus
Pseudoalteromonas
Pseudomonas
Psychrobacter
Psychromonas
Pyrobaculum
Pyrococcus
Ralstonia
Renibacterium
Rhizobium
Rhodobacter
Rhodococcus
Rhodoferax
Rhodopseudomonas
Rhodospirillum
Rhodothermus
Rickettsia
Robiginitalea
Roseiflexus
Roseobacter
Rothia
Rubrobacter
Ruegeria
Saccharomonospora
Saccharophagus
Saccharopolyspora
Salinibacter
Salinispora
Salmonella
Sanguibacter
Sebaldella
Segniliparus
Serratia
Shewanella
Shigella
Sideroxydans
Silicibacter
Sinorhizobium
Slackia
Sodalis
Solibacter
Sorangium
Sphaerobacter
Sphingobium
Sphingomonas
Sphingopyxis
Spirosoma
Stackebrandtia
Staphylococcus
Staphylothermus
Stenotrophomonas
Streptobacillus
Streptococcus
Streptomyces
Streptosporangium
Sulfolobus
Sulfurihydrogenibium
Sulfurospirillum
Sulfurovum
Symbiobacterium
Synechococcus
Synechocystis
Syntrophobacter
Syntrophomonas
Syntrophus
Teredinibacter
Thauera
Thermanaerovibrio
Thermincola
Thermoanaerobacter
Thermobaculum
Thermobifida
Thermobispora
Thermococcus
Thermocrinis
Thermodesulfovibrio
Thermofilum
Thermomicrobium
Thermomonospora
Thermoplasma
Thermoproteus
Thermosipho
Thermosphaera
Thermosynechococcus
Thermotoga
Thermus
Thioalkalivibrio
Thiobacillus
Thiomicrospira
Thiomonas
Tolumonas
Treponema
Trichodesmium
Tropheryma
Tsukamurella
Ureaplasma
Variovorax
Veillonella
Verminephrobacter
Vibrio
Wigglesworthia
Wolbachia
Wolinella
Xanthobacter
Xanthomonas
Xenorhabdus
Xylanimonas
Xylella
Yersinia
Zunongwangia
Zymomonas
alpha
cyanobacterium
uncultured
Select species:
Selected comparison genomes:
All Genomes
2. Specify an analysis method and any necessary options:
Find homologs for specific gene(s)
Get homolog list for a complete genome
Compare multiple genomes
Determine homology statistics
Browse homologs for specific gene(s) in the the reference genome that are found in the selected comparison genomes. Specify constraints to search for these genes to analyze below:
Gene name
Locus tag
Description
Start position range
to
For all genes in the reference genome, get a list of homologs in the selected comparison genomes meeting specified alignment score thresholds
Selecting only a couple Comparison Genomes is recommended for this analysis.
Select an output format:
HTML table
Tab delimited text file
Compare multiple genomes by determining genes with homologs in some genomes but not in others
Selecting only a couple Comparison Genomes is recommended for this analysis. Selecting 'All Genomes' is not allowed for this analysis.
Compare genomes based on the proportion of genes in the reference genome with homologs in the comparison genomes
3. Modify BLAST alignment score thresholds for finding gene homologs:
e-value <
1e-172
0.1
10
bit score >
600
200
20
% identity >
50
30
10
(select one)
4. Select Display Options
Limit number of hits to display
Limit results based on top hits
Limit results based on homolog cluster scores
List hit count in gene list
Display only first
hits
Show only top hits for each comparison genome
Show all hits for each comparison genome
Only show hits with a homolog clustering score of at least
Display number of BLAST hits
Display number of genomes with hits
© University of Washington 2008