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README for netblast (network-client BLAST)
Last updated 2/23/04
This README describes the BLAST client (blastcl3), which accesses the
NCBI BLAST search engine (version 2.2). The software behind BLAST
version 2.2 allows BLAST to handle new challenges posed by the
sequence databases. Updates to this software will continue in the
coming years.
1. Introduction
Blastcl3 can search all the sequences in a FASTA file, produce
one-to-many (master-slave) alignments in text or HTML format. It can
also perform searches against multiple databases. It also supports
organism-specific searches via the -u option, which functions like the
"Limit by Entrez Query Term" in the NCBI BLAST web pages. The old -l
option is removed. A full list of command-line options is given in
Appendix B.
The setup for NCBI network clients has been greatly simplified. If you
are not behind a firewall no further action is required. If you are
behind a firewall, and already use Sequin or Entrez, or if your system
administrator has already performed the setup, then you should be able
to start performing searches immediately. Otherwise, please refer to
'firewall.html' that is included with this archive for instructions on
firewall setups.
As an alternative to blastcl3, NCBI BLAST web server also supports
URL API, which uses url encoded command to interact with Blast.cgi to
"put" search requests and "get" search results. For details on the
standard commands, please refer to the online document at:
http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.pdf
2. Basic commandline for running blastcl3
Blastcl3 may be used to perform all five flavors of blast comparison.
For large blastn searches one can choose to use MEGABLAST algorithm
(-n T), which speeds up the search by concatenating the queries to
reduce database scan time. Please refer to Appendix B for the complete
list of program options for blastcl3. The list can also be displayed
by executing 'blastcl3 -' (the dash) command. A typical use of
blastcl3 is to perform a blastn search (nucleotide vs. nucleotide) of
a set of FASTA formatted sequences saved in a text file called QUERY:
blastcl3 -p blastn -d nr -i QUERY -o out.QUERY
The output is placed in the output file out.QUERY and the search is
performed against the 'nr' database. If a protein vs. protein search
is desired, 'blastn' should be replaced with 'blastp' etc. The
commandline below will search a query file named MY_QUERY against
protein nr database and place the result in a file called MY_QUEYR.out:
blastcl3 -p blastp -d nr -i MY_QUEYR -o MY_QUERY.out
One should issue the blastcl3 command under the blastcl3 containing
directory. For unix/linux system, ./ may need to be appended immediately
before the blastcl3 to instruct shell to look at the current directory.
One can also perform tther type of searches using different -p call
combined with correct -i/-d option value.
3. Commonly used options
The users need to use -i to specify the input file. Other options not
specified will assume default value. Often it is necessary to used
custom parameter values to ensure optimal results. The commonly used
blastcl3 options and their explanations are given below for your
reference.
-p Program Name [String]
Input should be one of "blastp", "blastn", "blastx",
"tblastn", or "tblastx".
-d Database [String]
default = nr
Multiple database names (bracketed by quotations) will be
accepted. An example would be:
-d "nr est"
which searches both the nr and est databases, presenting the
results as if one 'virtual' database consisting of all the
entries from both were searched. The statistics are based on
the combined 'virtual' database of nr and est. For supported
database list please refer to Appendix C.
-i Query File [File In]
default = stdin
The query sequences should be in FASTA format and the file
should be saved in plain text format. If multiple FASTA
entries are in the input file, all queries will be searched.
For query file format, see Appendix A.
-e Expectation value (E) [Real]
default = 10.0
Accepted formats are integer, decimal, fraction (1/6240),
and exponent (2e-64)
-o BLAST report Output File [File Out] Optional
default = stdout [screen]
-F Filter query sequence (DUST with blastn, SEG with others) [T/F]
default = T
BLAST 2.0 uses the dust low-complexity filter for blastn and
seg for the other programs. Both 'dust' and 'seg' are integral
parts of the NCBI toolkit and are accessed automatically.
If one uses "-F T" then normal filtering by seg or dust
(for blastn) occurs (likewise "-F F" means no filtering
whatsoever). The seg options can be changed by using:
-F "S 10 1.0 1.5"
which specifies a window of 10, locut of 1.0 and hicut of 1.5.
A coiled-coiled filter, based on the work of Lupas et al.
(Science, vol 252, pp. 1162-4 (1991)) and written by John
Kuzio (Wilson et al., J Gen Virol, vol. 76, p2923-32 (1995)),
may be invoked by specifying:
-F "C"
There are three parameters for this: window, cutoff (prob of a
coil-coil), and linker (distance between two coiled-coiled
regions that should be linked together). These are now set to
window: 22
cutoff: 40.0
linker: 32
One may also change the coiled-coiled parameters in a manner
analogous to that of seg:
-F "C 28 40.0 32" will change the window to 28.
One may also run both seg and coiled-coiled together by using
a ";":
-F "C;S"
Filtering by dust may also be specified by:
-F "D"
It is possible to specify that the masking should only be done
during the process of building the initial words by starting
the filtering command with 'm':
-F "m S"
which specifies that seg (with default arguments) should be
used for masking, but that the masking should only be done when
the words are being built. This masking option is available
with all filters.
-F "R"
This would invoke the human repeat filter to mask the human
repeat element present in the query sequences.
-F "V"
This would invoke the vector filter to mask the vector sequences
present in the query sequences.
-S Query strands to search against database (for blast[nx], and
tblastx).
[Integer]
3 is both, 1 is top [input strand], 2 is bottom [reverse complement]
default = 3
-T Produce HTML output [T/F]
default = F
-u Entrez query terms [Optional]
Some examples for how to use -u option:
-u mouse[organism]
This limits the search to sequences from mouse.
-u biomol_mrna[properties]
This limits the search to mRNA sequences.
-u "nucleotide_all[filter] NOT human[organism]"
This limits the search to all non-human entries.
For details on the terms, please refer to this web document:
http://www.ncbi.nlm.nih.gov:80/entrez/query/static/help/helpdoc.html
4. Firewall Settings
blastcl3 needs constant internet connection to NCBI blast servers to
function properly. There are extra setups if blastcl3 connects to
NCBI from behind a firewall.
First, one need to check with local network administrator to make sure
that the following IP address/port combinations are open in the
firewall configuration:
IP address Port
------------- ----
130.14.29.112 5861
130.14.29.112 5862
130.14.29.112 5863
This ensures that the appropriate path is open in the firewall through
which blastcl3 can make needed connections to NCBI server.
Second, one needs to set environment variables so that blastcl3 is
aware of the firewall setting. This can be achieved indirectly by
creating .ncbirc file (or ncbi.ini for Window machines) containing the
settings. This file should be placed in appropriate places, such as the
home directory for unix or linux system, or WINNT directory for Windows
machine. This file instructs blastcl3 to use the settings in the file,
rather than the default settings built into the program itself for
connecting to NCBI server.
The settings needed are the followings:
[CONN]
FIREWALL=TRUE
If one specifies it by using environment variables, use this:
CONN_FIREWALL=TRUE
5. FASTA Query file format
Query files with multiple query sequences should be put in this format
with defline in a separate line and the sequences put in 70-80
characters per line. NOTE the file should be in text format. If WORD
or other word processing program is used, make sure the file is saved
as text.
>query_sequence_1
MNTIRNSICLTIITMVLCGFLFPLAITLIGQIFFYQQANGSLITYDNRIVGSKLIGQHWTETRYFHGRPS
AVDYNMNPEKLYKNGVSSGGSNESNGNTELIARMKHHVKFGNSNVTIDAATSSGSGLDPHITVENALKQA
PRIADARHISTSRVADLIQHRKQRGVLTNDYVNVLELNIALDKMKD
>query_sequence_2
MAQPGPAPQPDVSLQQRVAELEKINAEFLRAQQQLEQEFNQKRAKFKELYLAKEEDLKRQNAVLQAAQDD
LGHLRTQLWEAQAEMENIKAIATVSENTKQEAIDEVKRQWREEVASLQAIMKETVRDYEHQFHLRLEQER
AQWAQYRESAEREIADLRRRLSEGQEEENLENEMKKAQEDAEKLRSVVMPMEKEIAALKDKLTEAEDKIK
ELEASKVKELNHYLEAEKSCRTDLEMYVAVLNTQKSVLQEDAEKLRKELHEVCHLLEQERQQHNQLKHTW
6. Complete list of blastcl3 arguments
The complete program options for blastcl3 are listed below for reference
purposes. Most of the parameters can be left out of the commandline.
In these cases, they will assume default settings, sufficient for normal
blast search purposes.
One can also generate this list by typing "blastcl3 -", without the quotes,
followed by a return key stroke. blastcl3 will print them on the screen.
-p Program Name [String]
-d Database [String]
default = nr
-i Query File [File In]
default = stdin
-e Expectation value (E) [Real]
default = 10.0
-m alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular,
9 = tabular with comment lines [Integer]
default = 0
-o BLAST report Output File [File Out] Optional
default = stdout
-F Filter query sequence (DUST with blastn, SEG with others)[String]
default = T
-G Cost to open a gap (zero invokes default behavior) [Integer]
default = 0
-E Cost to extend a gap (zero invokes default behavior) [Integer]
default = 0
-X X dropoff value for gapped alignment (in bits) (zero invokes
default behavior)
blastn 30, megablast 20, tblastx 0, all others 15 [Integer]
default = 0
-I Show GI's in deflines [T/F]
default = F
-q Penalty for a nucleotide mismatch (blastn only) [Integer]
default = -3
-r Reward for a nucleotide match (blastn only) [Integer]
default = 1
-v Number of database sequences to show one-line descriptions
for (V) [Integer]
default = 500
-b Number of database sequence to show alignments for (B) [Integer]
default = 250
-f Threshold for extending hits, default if zero
blastp 11, blastn 0, blastx 12, tblastn 13
tblastx 13, megablast 0 [Integer]
default = 0
-g Perfom gapped alignment (not available with tblastx) [T/F]
default = T
-Q Query Genetic code to use [Integer]
default = 1
-D DB Genetic code (for tblast[nx] only) [Integer]
default = 1
-a Number of processors to use [Integer]
default = 1
-O SeqAlign file [File Out] Optional
-J Believe the query defline [T/F]
default = F
-M Matrix [String]
default = BLOSUM62
-W Word size, default if zero (blastn 11, megablast 28, all others 3)
[Integer]
default = 0
-z Effective length of the database (use zero for the real size)
[Real]
default = 0
-K Number of best hits from a region to keep (off by default, if used
an value of 100 is recommended) [Integer]
default = 0
-Y Effective length of the search space (use zero for the real size)
[Real]
default = 0
-S Query strands to search against database (for blast[nx], and
tblastx) 3 is both, 1 is top, 2 is bottom [Integer]
default = 3
-T Produce HTML output [T/F]
default = F
-u Restrict search of database to results of Entrez2 lookup
[String] Optional
-U Use lower case filtering of FASTA sequence [T/F] Optional
default = F
-y X dropoff value for ungapped extensions in bits (0.0 invokes
default behavior) blastn 20, megablast 10, all others 7 [Real]
default = 0.0
-Z X dropoff value for final gapped alignment in bits (0.0 invokes
default behavior) blastn/megablast 50, tblastx 0, all others 25
[Integer]
default = 0
-R RPS Blast search [T/F]
default = F
-n MegaBlast search [T/F]
default = F
-L Location on query sequence [String] Optional
-A Multiple Hits window size, default if zero (blastn/megablast 0,
all others 40 [Integer]
default = 0
-w Frame shift penalty (OOF algorithm for blastx) [Integer]
default = 0
-t Length of the largest intron allowed in tblastn for linking HSPs
(0 disables linking) [Integer]
default = 0
Appendix. Currently supported databases
NOTE: all the database should be called with -d NAME, where the
NAME should be exactly as it appears in the lists given below!
A. General Nucleotide Sequence Databases
+--------+-----------------------------------------------------------+
|NAME |CONTENT |
+--------|-----------------------------------------------------------+
nr All GenBank+EMBL+DDBJ sequences (but no EST, STS,
GSS, or phase 0, 1 or 2 HTGS sequences). WGS entries are
also excluded. No longer "non-redundant".
est Database for entries from EST division of
GenBank+EMBL+DDBJ.
est_human Human subset of est.
est_mouse Mouse subset of est.
est_others ESTs other than human or mouse.
gss Genome Survey Sequence, includes single-pass genomic data,
exon-trapped sequences, and Alu PCR sequences.
htgs Unfinished High Throughput Genomic Sequences: phases 0, 1
and 2. Finished, phase 3 HTG sequences are in nr.
pat Nucleotides from the Patent division of GenBank.
month All new or revised GenBank+EMBL+DDBJ+PDB sequences
released updated in the last 30 days.
alu Select Alu repeats from REPBASE, suitable for masking
Alu repeats from query sequences.
sts Database of GenBank+EMBL+DDBJ sequences from STS Division.
chromosome Complete genomes, complete chromosome, or concatenated
genomic contigs form the NCBI Reference Sequence project.
UniVec The UniVec non-redundant vector fragment sequences.
wgs whole genome shotgun sequence assembly
+-----------+--------------------------------------------------------+
One can blast search a specific completed bacterial or archeal genomes
by searching the chromosome database and limit the search to that
microbe using -u option. For example, to search a query file QUERY
against Aquifex aeolicus genome, one can use the following commandline:
blastcl3 -p blastn -i QUERY -d chromosome -u "Aquifex aeolicus[orgn]" -o Out
For list of completed bacterial and archeal genomes, please visit:
http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/eub.html
http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/a_g.html
B. General peptide sequence databases
+-----------+--------------------------------------------------------+
|NAME |CONTENT |
+-----------+--------------------------------------------------------+
nr All non-redundant GenBank CDS translations + PDB
+ SwissProt + PIR + PRF. Non-redundant.
swissprot Last major release of the SWISS-PROT protein sequence
database (no updates)
pat Patent protein sequence database.
pdb Sequences derived from the 3-dimensional structure
records from PDB.
month All new or revised GenBank CDS translation + PDB +
SwissProt + PIR + PRF released in the last 30 days.
+-----------+--------------------------------------------------------+
C. Specialized Human Sequence Databases
C.1 Human genome related databases
+--------------------------+-----------------------------------------+
|NAME |CONTENT |
+--------------------------+-----------------------------------------+
hs_genome/genome default genome database
hs_genome/gnomon_prot Ab nitio (predicted) protein sequences
hs_genome/gnomon_rna Ab nitio (predicted) mRNA sequences
hs_genome/hs_bes human BAC end sequences
hs_genome/hs_est human EST sequences
hs_genome/hs_htg human HTG sequences
hs_genome/hs_refm RefSeq mRNA sequences
hs_genome/hs_refp RefSeq protein sequences
hs_genome/protein Build RNA
hs_genome/rna Build protein
Trace/Homo_Sapiens_EST EST Traces
Trace/Homo_Sapiens_Others Other Traces
+--------------------------+-----------------------------------------+
C.2 Human SNP databases
+--------------------------+-----------------------------------------+
|NAME |CONTENT |
+--------------------------+-----------------------------------------+
snp/snpch1.fas human snps mapped to Chromosome 1
snp/snpch2.fas human snps mapped to Chromosome 2
snp/snpch3.fas human snps mapped to Chromosome 3
snp/snpch4.fas human snps mapped to Chromosome 4
snp/snpch5.fas human snps mapped to Chromosome 5
snp/snpch6.fas human snps mapped to Chromosome 6
snp/snpch7.fas human snps mapped to Chromosome 7
snp/snpch8.fas human snps mapped to Chromosome 8
snp/snpch9.fas human snps mapped to Chromosome 9
snp/snpch10.fas human snps mapped to Chromosome 10
snp/snpch11.fas human snps mapped to Chromosome 11
snp/snpch12.fas human snps mapped to Chromosome 12
snp/snpch13.fas human snps mapped to Chromosome 13
snp/snpch14.fas human snps mapped to Chromosome 14
snp/snpch15.fas human snps mapped to Chromosome 15
snp/snpch16.fas human snps mapped to Chromosome 16
snp/snpch17.fas human snps mapped to Chromosome 17
snp/snpch18.fas human snps mapped to Chromosome 18
snp/snpch19.fas human snps mapped to Chromosome 19
snp/snpch20.fas human snps mapped to Chromosome 20
snp/snpch21.fas human snps mapped to Chromosome 21
snp/snpch22.fas human snps mapped to Chromosome 22
snp/snpchX.fas. human snps mapped to Chromosome X
snp/snpchY.fas.nsq human snps mapped to Chromosome Y
snp/snpchMulti.fas human snps mapped to multiple chromosomes
snp/snpchNotOn.fas human snps not yet mapped to chromosome
snp/snpchMasked.fas repeat masked human snps
snp/snp All the above
+--------------------------+-----------------------------------------+
D. Specialized Mouse Sequence databases
+--------------------------+----------------------------------------+
|NAME |CONTENT |
+--------------------------+----------------------------------------+
mouse_contig/genome current mouse genome assembly
mouse_contig/gnomon_prot predicted proteins from the above genome
mouse_contig/gnomon_rna predicted mRNAs from the above genome
mouse_contig/mm_bes mouse bac end sequences (from gss)
mouse_contig/mm_est mouse est (est_mouse)
mouse_contig/mm_htg mouse htgs sequeneces, including phase 3
mouse_contig/mm_refm mouse refseq mRNA (updated daily)
mouse_contig/mm_refp mouse refseq protin (updated daily)
mouse_contig/protein mouse build mRNAs
mouse_contig/rna mouse proteins from build mRNAs
Trace/Mus_Musculus_EST EST Traces
Trace/Mus_Musculus_others Other Traces
+--------------------------+-----------------------------------------+
E. Specialized Rat Sequence databases
+---------------------------+----------------------------------------+
|NAME |CONTENT |
+---------------------------+----------------------------------------+
rn_genome/genome latest public rat genome build
rn_genome/gnomon_prot proteins from predicted mRNAs
rn_genome/gnomon_rna mRNAs predicted off the genome build
rn_genome/protein proteins from build mRNA
rn_genome/rn_bes rat BAC end sequences
rn_genome/rn_est rat EST sequences
rn_genome/rn_htg rat htgs, including phase 3
rn_genome/rn_refm rat refseq mRNA, updated daily
rn_genome/rn_refp rat refseq protein, updated daily
rn_genome/rna rat build mRNAs
rn_genome/wgs_contigs rat wgs contigs
+--------------------------+-----------------------------------------+
F. Specialized Zebra fish and Puffer fish Sequence databases
+---------------------------+----------------------------------------+
|NAME |CONTENT |
+---------------------------+----------------------------------------+
dr_genome/dr_mrna Zebra fish mRNA
dr_genome/dr_htg HTGS phase 0, 1, 2, or 3 sequences.
dr_genome/dr_est subset of Zebra fish EST from the EST database
dr_genome/dr_refm Reference mRNAs from RefSeq project
dr_genome/dr_refp Reference Proteins from RefSeq project
Trace/Danio_Rerio_WGS Zebra fish whole genome shotgun Traces
Trace/Danio_Rerio_EST Zebra fish EST Traces
genomes/fugu Fugu genome
+---------------------------+----------------------------------------+
G. Specialized Insects and Worm Sequence databases
+---------------------------+----------------------------------------+
|NAME |CONTENT |
+---------------------------+----------------------------------------+
genomes/ag_mrna Mosquito mRNA predicted off the genome
genomes/agambiae Mosquito genome scaffold
genomes/agambiae Mosquito proteins from predicted mRNA
genomes/dm Drosophila melanogaster mRNAs
genomes/dm Drosophila melanogaster proteins
genomes/dm_genomic Drosophila melanogaster genomic contigs
genomes/dpWGS Drosophila pseudoobscura WGS contigs
genomes/hbWGS honeybee wgs contigs
genomes/insects_genomic insects' genomic sequences
genomes/c_briggsae C. briggsae genomic sequences
genomes/c_elegans C. elegans predicted mRNA
genomes/c_elegans C. elegans protein from predicted mRNA
genomes/c_elegans_chr C. elegans chromosomes
+---------------------------+----------------------------------------+
H. Specialized Fungi, Plants genome database
+---------------------------+----------------------------------------+
|NAME |CONTENT |
+---------------------------+----------------------------------------+
genomes/Giardia Giardia lamblia genomic sequences
genomes/Giardia Giardia lamblia protein sequences
genomes/anidulans Aspergillus nidulans DNA sequences
genomes/anidulans Aspergillus nidulans protein sequences
genomes/cionaWGS Ciona intestinalis wgs sequences
genomes/p_falciparum P. falciparum genome
genomes/p_falciparum P. falciparum protein
genomes/p_yoelii P. yoelii genome
genomes/p_yoelii P. yoelii protein
genomes/s_bayanusMIT S. bayanus genome(MIT)
genomes/s_bayanusWashU S. bayanus genome(WUSTL)
genomes/s_castellii S. castellii genome
genomes/s_kluyveri S. kluuyveri genome
genomes/s_kudriavzevii S. kudriavzevii genome
genomes/s_mikataeMIT S. mikatae genome (MIT)
genomes/s_mikataeWashU S. mikatae genome (WUSTL)
genomes/s_paradoxus S. paradoxus genome
genomes/scerevis S. cerevisiae genome
genomes/scerevis S. cerevisiae proteins
genomes/spombe S. pombe genome
genomes/spombe S. pombe proteins
genomes/nc_comp Neurospora genome
genomes/nc_mrna Neurospora mRNAs
genomes/nc_prot Neurospora proteins
genomes/fungi all fungal genomes
genomes/fungi all predicted fungal proteins
genomes/fungi_mrna all predicted fungal mRNAs
genomes/ara Arabidopsis mRNAs
genomes/ara.pal Arabidopsis proteins
genomes/ara_chr Arabidopsis chromosome
genomes/ara_clone Arabidopsis genomic clones
genomes/barley barley mRNA sequences
genomes/barley_clone barley genomic clones
genomes/barley_est barley est entries
genomes/barley_sts barley sts entries
genomes/corn corn mRNA sequences
genomes/corn_clone corn genomic clones
genomes/corn_est corn est entries
genomes/corn_gss corn gss entries
genomes/corn_patnt corn patent nucleotides
genomes/corn_sts corn sts entries
genomes/oat oat mRNAs
genomes/oat_clone oat genomic clones
genomes/oat_est oat est entries
genomes/oat_sts oat sts entries
genomes/rice ?? rice mRNA sequences
genomes/rice rice protein sequences
genomes/riceChWGS rice wgs assemblies
genomes/rice_clone rice genomic contigs
genomes/rice_est rice est entries
genomes/rice_gss rice gss entries
genomes/rice_htgs rice htgs entries
genomes/rice_mrna rice mRNA sequences
genomes/rice_sts rice sts entries
genomes/soybean Glycine max mRNA sequences
genomes/soybean_clone Glycine max genomic clones
genomes/soybean_est Glycine max est entries
genomes/tomato Tomato mRNA sequences
genomes/tomato_est Tomato est entries
genomes/wheat Wheat mRNA sequences
genomes/wheat_clone Wheat genomic clones
genomes/wheat_est Wheat est entries
genomes/wheat_gss Wheat gss entries
genomes/wheat_sts Wheat sts entries
genomes/plant genomic sequences for plants
listed here
+---------------------------+------------------------------------+
I. Microbial, archaeal, and lower eukaryotic genome databases
+------------------+---------------------------------------------+
| NAME | CONTENT |
+------------------+---------------------------------------------+
Microbial/100226 Streptomyces coelicolor A3(2)
Microbial/100379 Onion yellows phytoplasma
Microbial/103690 Nostoc sp. PCC 7120
Microbial/1063 Rhodobacter sphaeroides
Microbial/1076 Rhodopseudomonas palustris
Microbial/107806 Buchnera aphidicola str. APS
(Acyrthosiphon pisum)
Microbial/1085 Rhodospirillum rubrum
Microbial/1108 Chloroflexus aurantiacus
Microbial/111955 Sulfolobus tokodaii
Microbial/1148 Synechocystis sp. PCC 6803
Microbial/115711 Chlamydophila pneumoniae AR39
Microbial/115713 Chlamydophila pneumoniae CWL029
Microbial/117 Pirellula sp.
Microbial/119072 Thermoanaerobacter tengcongensis
Microbial/119219 Ralstonia metallidurans
Microbial/122586 Neisseria meningitidis MC58
Microbial/122587 Neisseria meningitidis Z2491
Microbial/1282 Staphylococcus epidermidis
Microbial/1299 Deinococcus radiodurans
Microbial/1309 Streptococcus mutans
Microbial/1336 Streptococcus equi
Microbial/134537 Burkholderia fungorum
Microbial/1352 Enterococcus faecium
Microbial/135720 Neisseria meningitidis serogroup C
Microbial/1360 Lactococcus lactis subsp. lactis
Microbial/13773 Pyrobaculum aerophilum
Microbial/138677 Chlamydophila pneumoniae J138
Microbial/139 Borrelia burgdorferi
Microbial/1422 Geobacillus stearothermophilus
Microbial/1423 Bacillus subtilis
Microbial/145262 Methanothermobacter thermautotrophicus
Microbial/1488 Clostridium acetobutylicum
Microbial/1496 Clostridium difficile
Microbial/1502 Clostridium perfringens
Microbial/155864 Escherichia coli O157:H7 EDL933
Microbial/155919 Xylella fastidiosa Dixon
Microbial/155920 Xylella fastidiosa Ann-1
Microbial/156889 Magnetococcus sp. MC-1
Microbial/158878 Staphylococcus aureus subsp. aureus Mu50
Microbial/158879 Staphylococcus aureus subsp. aureus N315
Microbial/159087 Dechloromonas aromatica RCB
Microbial/159288 Staphylococcus aureus subsp. aureus 252
Microbial/159289 Staphylococcus aureus subsp. aureus 476
Microbial/1596 Lactobacillus gasseri
Microbial/160 Treponema pallidum
Microbial/160488 Pseudomonas putida KT2440
Microbial/160489 Pseudomonas putida PRS1
Microbial/160490 Streptococcus pyogenes M1 GAS
Microbial/160491 Streptococcus pyogenes Manfredo
Microbial/160492 Xylella fastidiosa 9a5c
Microbial/163164 Wolbachia endosymbiont of Drosophila
melanogaster
Microbial/1642 Listeria innocua
Microbial/164513 Mycobacterium tuberculosis 210
Microbial/164609 Wigglesworthia glossinidia endosymbiont
of Glossina brevipalpis
Microbial/167539 Prochlorococcus marinus subsp.
marinus str. CCMP1375
Microbial/167879 Colwellia psychrerythraea 34H
Microbial/1679 Bifidobacterium longum biovar Longum
Microbial/169963 Listeria monocytogenes EGD-e
Microbial/170187 Streptococcus pneumoniae TIGR4
Microbial/171101 Streptococcus pneumoniae R6
Microbial/1717 Corynebacterium diphtheriae
Microbial/1718 Corynebacterium glutamicum
Microbial/176279 Staphylococcus epidermidis RP62A
Microbial/176280 Staphylococcus epidermidis ATCC 12228
Microbial/176281 Listeria monocytogenes ATCC 19115
Microbial/1765 Mycobacterium bovis
Microbial/1769 Mycobacterium leprae
Microbial/178306 Pyrobaculum aerophilum str. IM2
Microbial/178328 Salmonella typhimurium TR7095
Microbial/180454 Anopheles gambiae str. PEST
Microbial/180835 Agrobacterium tumefaciens str. C58
(U. Washington)
Microbial/181661 Agrobacterium tumefaciens str. C58
(Cereon)
Microbial/182082 Chlamydophila pneumoniae TW-183
Microbial/182710 Oceanobacillus iheyensis
Microbial/183190 Xylella fastidiosa Temecula1
Microbial/184922 Giardia lamblia ATCC 50803
Microbial/186103 Streptococcus pyogenes MGAS8232
Microbial/186497 Pyrococcus furiosus DSM 3638
Microbial/187410 Yersinia pestis KIM
Microbial/187420 Methanothermobacter thermautotrophicus
str. Delta H
Microbial/188 Magnetospirillum magnetotacticum
Microbial/188937 Methanosarcina acetivorans C2A
Microbial/189423 Streptococcus pneumoniae 670
Microbial/189518 Leptospira interrogans serovar lai
str. 56601
Microbial/190192 Methanopyrus kandleri AV19
Microbial/190304 Fusobacterium nucleatum subsp.
nucleatum ATCC 25586
Microbial/190485 Xanthomonas campestris pv. Campestris
str. ATCC 33913
Microbial/190486 Xanthomonas axonopodis pv. citri str. 306
Microbial/190650 Caulobacter crescentus CB15
Microbial/191218 Bacillus anthracis str. A2012
Microbial/192222 Campylobacter jejuni subsp. jejuni
NCTC 11168
Microbial/192952 Methanosarcina mazei Goe1
Microbial/193567 Streptococcus pyogenes SSI-1
Microbial/194439 Chlorobium tepidum TLS
Microbial/195099 Campylobacter jejuni RM1221
Microbial/195102 Clostridium perfringens str. 13
Microbial/195103 Clostridium perfringens ATCC 13124
Microbial/196164 Corynebacterium efficiens YS-314
Microbial/196600 Vibrio vulnificus YJ016
Microbial/196620 Staphylococcus aureus subsp. aureus MW2
Microbial/196627 Corynebacterium glutamicum ATCC 13032
Microbial/197 Campylobacter jejuni
Microbial/197221 Thermosynechococcus elongatus BP-1
Microbial/198094 Bacillus anthracis str. Ames
Microbial/198214 Shigella flexneri 2a str. 301
Microbial/198215 Shigella flexneri 2a str. 2457T
Microbial/198466 Streptococcus pyogenes MGAS315
Microbial/198628 Erwinia chrysanthemi str. 3937
Microbial/198804 Buchnera aphidicola str. Sg
(Schizaphis graminum)
Microbial/199310 Escherichia coli CFT073
Microbial/2021 Thermobifida fusca
Microbial/203119 Clostridium thermocellum ATCC 27405
Microbial/203120 Leuconostoc mesenteroides subsp.
mesenteroides ATCC 8293
Microbial/203122 Microbulbifer degradans 2-40
Microbial/203123 Oenococcus oeni MCW
Microbial/203124 Trichodesmium erythraeum IMS101
Microbial/203267 Tropheryma whipplei str. Twist
Microbial/203275 Tannerella forsythensis ATCC 43037
Microbial/203907 Candidatus Blochmannia floridanus
Microbial/204722 Brucella suis 1330
Microbial/205913 Bifidobacterium longum DJO10A
Microbial/205914 Haemophilus somnus 129PT
Microbial/205918 Pseudomonas syringae pv. syringae B728a
Microbial/205919 Bacillus anthracis str. KrugerB
Microbial/205920 Ehrlichia chaffeensis str. Arkansas
Microbial/205921 Streptococcus agalactiae A909
Microbial/205922 Pseudomonas fluorescens PfO-1
Microbial/206672 Bifidobacterium longum NCC2705
Microbial/207559 Desulfovibrio desulfuricans G20
Microbial/208435 Streptococcus agalactiae 2603V/R
Microbial/208963 Pseudomonas aeruginosa UCBPP-PA14
Microbial/208964 Pseudomonas aeruginosa PAO1
Microbial/209261 Salmonella enterica subsp.
enterica serovar Typhi Ty2
Microbial/2097 Mycoplasma genitalium
Microbial/209841 Actinobacillus pleuropneumoniae serovar 7
Microbial/209882 Fusobacterium nucleatum subsp.
vincentii ATCC 49256
Microbial/210007 Streptococcus mutans UA159
Microbial/2104 Mycoplasma pneumoniae
Microbial/2107 Mycoplasma pulmonis
Microbial/2111 Mycoplasma arthritidis
Microbial/211110 Streptococcus agalactiae NEM316
Microbial/211586 Shewanella oneidensis MR-1
Microbial/212042 Anaplasma phagocytophilum HZ
Microbial/212045 Bacillus anthracis str. WesternNA
Microbial/212717 Clostridium tetani E88
Microbial/2130 Ureaplasma urealyticum
Microbial/214092 Yersinia pestis CO92
Microbial/214684 Cryptococcus neoformans var.
neoformans JEC21
Microbial/214688 Gemmata obscuriglobus UQM 2246
Microbial/216591 Burkholderia cenocepacia J2315
Microbial/216592 Escherichia coli 042
Microbial/216593 Escherichia coli E2348
Microbial/216594 Mycobacterium marinum M
Microbial/216595 Pseudomonas fluorescens SBW25
Microbial/216596 Rhizobium leguminosarum bv. viciae 3841
Microbial/216597 Salmonella typhimurium SL1344
Microbial/216598 Shigella dysenteriae M131649
Microbial/216599 Shigella sonnei 53G
Microbial/216600 Streptococcus pneumoniae 23F
Microbial/216895 Vibrio vulnificus CMCP6
Microbial/218491 Erwinia carotovora subsp.
atroseptica SCRI1043
Microbial/218493 Salmonella bongori 12149
Microbial/218494 Streptococcus suis P1/7
Microbial/218495 Streptococcus uberis 0140J
Microbial/218496 Tropheryma whipplei TW08/27
Microbial/218497 Chlamydophila abortus S26/3
Microbial/2190 Methanocaldococcus jannaschii
Microbial/220664 Pseudomonas fluorescens Pf-5
Microbial/220668 Lactobacillus plantarum WCFS1
Microbial/2208 Methanosarcina barkeri
Microbial/221109 Oceanobacillus iheyensis HTE831
Microbial/222523 Bacillus cereus ATCC 10987
Microbial/222891 Neorickettsia sennetsu str. Miyayama
Microbial/222929 Coccidioides posadasii C735
Microbial/223283 Pseudomonas syringae pv.
tomato str. DC3000
Microbial/2234 Archaeoglobus fulgidus
Microbial/223926 Vibrio parahaemolyticus RIMD 2210633
Microbial/224308 Bacillus subtilis subsp.
subtilis str. 168
Microbial/224324 Aquifex aeolicus VF5
Microbial/224325 Archaeoglobus fulgidus DSM 4304
Microbial/224326 Borrelia burgdorferi B31
Microbial/224911 Bradyrhizobium japonicum USDA 110
Microbial/224914 Brucella melitensis 16M
Microbial/224915 Buchnera aphidicola str. Bp
(Baizongia pistaciae)
Microbial/226125 Saccharomyces paradoxus NRRL Y-17217
Microbial/226126 Saccharomyces mikatae IFO 1815
Microbial/226127 Saccharomyces bayanus MCYC 623
Microbial/226185 Enterococcus faecalis V583
Microbial/226186 Bacteroides thetaiotaomicron VPI-5482
Microbial/226230 Saccharomyces kudriavzevii IFO 1802
Microbial/226231 Saccharomyces bayanus 623-6C
Microbial/226301 Saccharomyces castellii NRRL Y-12630
Microbial/226302 Saccharomyces kluyveri NRRL Y-12651
Microbial/226900 Bacillus cereus ATCC 14579
Microbial/227321 Aspergillus nidulans FGSC A4
Microbial/227377 Coxiella burnetii RSA 493
Microbial/227882 Streptomyces avermitilis MA-4680
Microbial/227941 Chlamydophila caviae GPIC
Microbial/228399 Actinobacillus pleuropneumoniae serovar 1
str. 4074
Microbial/228400 Haemophilus somnus 2336
Microbial/228405 Hyphomonas neptunium ATCC 15444
Microbial/228410 Nitrosomonas europaea ATCC 19718
Microbial/2287 Sulfolobus solfataricus
Microbial/228908 Nanoarchaeum equitans Kin4-M
Microbial/229533 Gibberella zeae PH-1
Microbial/2303 Thermoplasma acidophilum
Microbial/233150 Mycoplasma gallisepticum R
Microbial/233412 Haemophilus ducreyi 35000HP
Microbial/233413 Mycobacterium bovis AF2122/97
Microbial/2336 Thermotoga maritima
Microbial/234826 Anaplasma marginale str. St. Maries
Microbial/235279 Helicobacter hepaticus ATCC 51449
Microbial/235443 Cryptococcus neoformans var. grubii H99
Microbial/237631 Ustilago maydis 521
Microbial/238030 Pasteuria nishizawae str. North American
Microbial/24 Shewanella putrefaciens
Microbial/240176 Coprinopsis cinerea okayama7#130
Microbial/242507 Magnaporthe grisea 70-15
Microbial/242619 Porphyromonas gingivalis W83
Microbial/243090 Pirellula sp. 1
Microbial/243159 Acidithiobacillus ferrooxidans ATCC 23270
Microbial/243160 Burkholderia mallei ATCC 23344
Microbial/243164 Dehalococcoides ethenogenes 195
Microbial/243230 Deinococcus radiodurans R1
Microbial/243231 Geobacter sulfurreducens PCA
Microbial/243233 Methylococcus capsulatus str. Bath
Microbial/243243 Mycobacterium avium 104
Microbial/243265 Photorhabdus luminescens subsp.
laumondii TTO1
Microbial/243272 Mycoplasma arthritidis 158L3-1
Microbial/243275 Treponema denticola ATCC 35405
Microbial/243276 Treponema pallidum subsp.
pallidum str. Nichols
Microbial/243277 Vibrio cholerae O1 biovar eltor
str. N16961
Microbial/243365 Chromobacterium violaceum ATCC 12472
Microbial/246194 Carboxydothermus hydrogenoformans Z-2901
Microbial/246195 Dichelobacter nodosus VCS1703A
Microbial/246196 Mycobacterium smegmatis MC2
Microbial/246197 Myxococcus xanthus DK 1622
Microbial/246198 Prevotella intermedia 17
Microbial/246199 Ruminococcus albus 8
Microbial/246200 Silicibacter pomeroyi DSS-3
Microbial/246201 Streptococcus mitis NCTC 12261
Microbial/246202 Streptococcus sobrinus 6715
Microbial/254945 Ehrlichia ruminantium str. Welgevonden
Microbial/257310 Bordetella bronchiseptica RB50
Microbial/257313 Bordetella pertussis Tohama I
Microbial/257314 Lactobacillus johnsonii NCC 533
Microbial/258594 Rhodopseudomonas palustris CGA009
Microbial/259536 Psychrobacter sp. 273-4
Microbial/262316 Mycobacterium avium subsp.
paratuberculosis str. k10
Microbial/262727 Haemophilus influenzae R2846
Microbial/262728 Haemophilus influenzae R2866
Microbial/28227 Mycoplasma penetrans
Microbial/28232 Geobacter metallireducens
Microbial/28450 Burkholderia pseudomallei
Microbial/287 Pseudomonas aeruginosa
Microbial/29292 Pyrococcus abyssi
Microbial/29390 Streptococcus gordonii str. Challis
Microbial/294 Pseudomonas fluorescens
Microbial/29459 Brucella melitensis
Microbial/29461 Brucella melitensis biovar Suis
Microbial/305 Ralstonia solanacearum
Microbial/31033 Takifugu rubripes
Microbial/32049 Synechococcus sp. PCC 7002
Microbial/33072 Gloeobacter violaceus
Microbial/33178 Aspergillus terreus
Microbial/34054 Yersinia enterocolitica (type 0:8)
Microbial/354 Azotobacter vinelandii
Microbial/35793 Rickettsia sibirica
Microbial/36329 Plasmodium falciparum 3D7
Microbial/36826 Clostridium botulinum A
Microbial/36870 Wigglesworthia glossinidia
endosymbiont of Glossina brevipalpis
Microbial/3702 Arabidopsis thaliana
Microbial/375 Bradyrhizobium japonicum
Microbial/38081 Pneumocystis carinii
Microbial/381 Mesorhizobium loti
Microbial/382 Sinorhizobium meliloti
Microbial/40325 Actinobacillus pleuropneumoniae serovar 1
Microbial/42068 Pneumocystis jirovecii
Microbial/42897 Shigella flexneri 2a
Microbial/44101 Mycoplasma mycoides subsp. mycoides SC
Microbial/44294 Actinobacillus pleuropneumoniae serovar 5
Microbial/446 Legionella pneumophila
Microbial/47834 Spiroplasma kunkelii
Microbial/485 Neisseria gonorrhoeae
Microbial/48935 Novosphingobium aromaticivorans
Microbial/4896 Schizosaccharomyces pombe
Microbial/4932 Saccharomyces cerevisiae
Microbial/49338 Desulfitobacterium hafniense
Microbial/50339 Thermoplasma volcanium
Microbial/5067 Aspergillus parasiticus
Microbial/5085 Aspergillus fumigatus
Microbial/5141 Neurospora crassa
Microbial/51511 Ciona savignyi
Microbial/518 Bordetella bronchiseptica
Microbial/519 Bordetella parapertussis
Microbial/520 Bordetella pertussis
Microbial/5207 Filobasidiella neoformans
Microbial/5306 Phanerochaete chrysosporium
Microbial/53953 Pyrococcus horikoshii
Microbial/54388 Salmonella paratyphi
Microbial/5476 Candida albicans
Microbial/5514 Fusarium sporotrichioides
Microbial/556 Erwinia chrysanthemi
Microbial/56636 Aeropyrum pernix
Microbial/5691 Trypanosoma brucei
Microbial/5693 Trypanosoma cruzi
Microbial/573 Klebsiella pneumoniae
Microbial/5759 Entamoeba histolytica
Microbial/5807 Cryptosporidium parvum
Microbial/5811 Toxoplasma gondii
Microbial/5823 Plasmodium berghei strain ANKA
Microbial/5825 Plasmodium chabaudi
Microbial/5855 Plasmodium vivax
Microbial/5861 Plasmodium yoelii
Microbial/5865 Babesia bovis
Microbial/5874 Theileria annulata
Microbial/5875 Theileria parva
Microbial/592 Salmonella enteritidis
Microbial/59374 Fibrobacter succinogenes subsp.
succinogenes S85
Microbial/59919 Prochlorococcus marinus subsp.
pastoris str. CCMP1986
Microbial/6035 Encephalitozoon cuniculi
Microbial/6182 Schistosoma japonicum
Microbial/6183 Schistosoma mansoni
Microbial/6238 Caenorhabditis briggsae
Microbial/6239 Caenorhabditis elegans
Microbial/6279 Brugia malayi
Microbial/632 Yersinia pestis
Microbial/63363 Aquifex aeolicus
Microbial/63737 Nostoc punctiforme
Microbial/64091 Halobacterium sp. NRC-1
Microbial/666 Vibrio cholerae
Microbial/672 Vibrio vulnificus
Microbial/6943 Amblyomma americanum
Microbial/714 Actinobacillus actinomycetemcomitans
Microbial/71421 Haemophilus influenzae Rd KW20
Microbial/7159 Aedes aegypti
Microbial/7160 Aedes albopictus
Microbial/7162 Ochlerotatus triseriatus
Microbial/7227 Drosophila melanogaster
Microbial/7237 Drosophila pseudoobscura
Microbial/730 Haemophilus ducreyi
Microbial/73239 Plasmodium yoelii yoelii
Microbial/74547 Prochlorococcus marinus str. MIT 9313
Microbial/7460 Apis mellifera
Microbial/747 Pasteurella multocida
Microbial/7719 Ciona intestinalis
Microbial/781 Rickettsia conorii
Microbial/782 Rickettsia prowazekii
Microbial/783 Rickettsia rickettsii
Microbial/813 Chlamydia trachomatis
Microbial/817 Bacteroides fragilis
Microbial/83331 Mycobacterium tuberculosis CDC1551
Microbial/83332 Mycobacterium tuberculosis H37Rv
Microbial/83333 Escherichia coli K12
Microbial/83334 Escherichia coli O157:H7
Microbial/83554 Chlamydophila psittaci
Microbial/83560 Chlamydia muridarum
Microbial/837 Porphyromonas gingivalis
Microbial/844 Wolinella succinogenes
Microbial/84588 Synechococcus sp. WH 8102
Microbial/85569 Salmonella typhimurium DT104
Microbial/85962 Helicobacter pylori 26695
Microbial/85963 Helicobacter pylori J99
Microbial/86665 Bacillus halodurans
Microbial/882 Desulfovibrio vulgaris subsp.
vulgaris str. Hildenborough
Microbial/90370 Salmonella enterica subsp.
enterica serovar Typhi
Microbial/915 Nitrosomonas europaea
Microbial/93061 Staphylococcus aureus subsp.
aureus NCTC 8325
Microbial/93062 Staphylococcus aureus subsp. aureus COL
Microbial/959 Bdellovibrio bacteriovorus
Microbial/97393 Ferroplasma acidarmanus
Microbial/98360 Salmonella enterica subsp.
enterica serovar Dublin
Microbial/985 Cytophaga hutchinsonii
Microbial/99287 Salmonella typhimurium LT2
+------------------+-------------------------------------------+
J.Trace Databases
+-----------------------------------------------------+------------+
|NAME | CONTENT* |
+-----------------------------------------------------+------------+
Trace/Acidithiobacillus_Ferrooxidans_Atcc_23270_WGS
Trace/Aedes_Aegypti_OTHER
Trace/Anopheles_Gambiae_OTHER
Trace/Anopheles_Gambiae_WGS
Trace/Apis_Mellifera_OTHER
Trace/Apis_Mellifera_WGS
Trace/Archaeoglobus_Fulgidus_Dsm_4304_WGS
Trace/Artibeus_Jamaicensis_OTHER
Trace/Aspergillus_Flavus_OTHER
Trace/Aspergillus_Fumigatus_WGS
Trace/Aspergillus_Nidulans_WGS
Trace/Aspergillus_Parasiticus_OTHER
Trace/Aspergillus_Terreus_WGS
Trace/Atelerix_Albiventris_OTHER
Trace/Bacillus_Anthracis_Str__A0039_OTHER
Trace/Bacillus_Anthracis_Str__A01055_OTHER
Trace/Bacillus_Anthracis_Str__A2012_WGS
Trace/Bacillus_Anthracis_Str__Ames_0581_OTHER
Trace/Bacillus_Anthracis_Str__Ames_WGS
Trace/Bacillus_Anthracis_Str__France_OTHER
Trace/Bacillus_Anthracis_Str__Kruger_B_OTHER
Trace/Bacillus_Anthracis_Str__Vollum_OTHER
Trace/Bacillus_Anthracis_Str__Western_North_America_OTHER
Trace/Bacillus_Cereus_Atcc_10987_WGS
Trace/Borrelia_Burgdorferi_B31_WGS
Trace/Bos_Taurus_EST
Trace/Bos_Taurus_OTHER
Trace/Botryllus_Schlosseri_OTHER
Trace/Branchiostoma_Floridae_OTHER
Trace/Brassica_Oleracea_WGS
Trace/Brucella_Suis_1330_OTHER
Trace/Burkholderia_Mallei_Atcc_23344_WGS
Trace/Caenorhabditis_Briggsae_WGS
Trace/Callicebus_Moloch_OTHER
Trace/Callithrix_Jacchus_OTHER
Trace/Campylobacter_Jejuni_Rm1221_WGS
Trace/Canis_Familiaris_OTHER
Trace/Canis_Familiaris_WGS
Trace/Carollia_Perspicillata_OTHER
Trace/Cercopithecus_Aethiops_OTHER
Trace/Chlamydia_Muridarum_Nigg_WGS
Trace/Chlamydomonas_Reinhardtii_OTHER
Trace/Chlamydomonas_Reinhardtii_WGS
Trace/Chlamydophila_Caviae_Gpic_WGS
Trace/Chlamydophila_Pneumoniae_Ar39_WGS
Trace/Chlorobium_Tepidum_Tls_WGS
Trace/Cicer_Arietinum_OTHER
Trace/Ciona_Intestinalis_OTHER
Trace/Ciona_Intestinalis_WGS
Trace/Ciona_Savignyi_WGS.00
Trace/Ciona_Savignyi_WGS.01
Trace/Clostridium_Perfringens_Atcc_13124_WGS
Trace/Coccidioides_Immitis_WGS
Trace/Colwellia_Psychrerythraea_34h_WGS
Trace/Coprinus_Cinereus_WGS
Trace/Coxiella_Burnetii_Rsa_493_WGS
Trace/Cryptococcus_Neoformans_Serotype_A_WGS
Trace/Danio_Rerio_EST
Trace/Danio_Rerio_OTHER
Trace/Dasypus_Novemcinctus_OTHER
Trace/Dehalococcoides_Ethenogenes_195_WGS
Trace/Didelphis_Virginiana_OTHER
Trace/Drosophila_Melanogaster_OTHER
Trace/Drosophila_Pseudoobscura_EST
Trace/Drosophila_Pseudoobscura_OTHER
Trace/Drosophila_Pseudoobscura_WGS
Trace/Drosophila_Simulans_WGS
Trace/Drosophila_Virilis_OTHER
Trace/Drosophila_Yakuba_WGS
Trace/Ehrlichia_Chaffeensis_Str__Arkansas_WGS
Trace/Emericella_Nidulans_OTHER
Trace/Enterococcus_Faecalis_V583_WGS
Trace/Equus_Caballus_OTHER
Trace/Euprymna_Scolopes_EST
Trace/Felis_Catus_OTHER
Trace/Gallus_Gallus_OTHER
Trace/Gallus_Gallus_WGS
Trace/Geobacter_Sulfurreducens_Pca_WGS
Trace/Gibberella_Zeae_WGS
Trace/Glycine_Max_EST
Trace/Gopherus_Agassizii_OTHER
Trace/Gorilla_Gorilla_OTHER
Trace/Homo_Sapiens_EST
Trace/Homo_Sapiens_OTHER
Trace/Homo_Sapiens_WGS
Trace/Lemur_Catta_OTHER
Trace/Macaca_Mulatta_EST
Trace/Macaca_Mulatta_OTHER
Trace/Macaca_Mulatta_WGS
Trace/Macropus_Eugenii_OTHER
Trace/Magnaportha_Grisea_WGS
Trace/Medicago_Truncatula_OTHER
Trace/Medicago_Truncatula_WGS
Trace/Mesoplasma_Florum_WGS
Trace/Methanosarcina_Acetivorans_WGS
Trace/Methylococcus_Capsulatus_Str__Bath_WGS
Trace/Microcebus_Murinus_OTHER
Trace/Monodelphis_Domestica_OTHER
Trace/Monodelphis_Domestica_WGS
Trace/Muntiacus_Muntjak_Vaginalis_OTHER
Trace/Mus_Musculus_EST
Trace/Mus_Musculus_OTHER
Trace/Mus_Musculus_WGS
Trace/Mycobacterium_Tuberculosis_Cdc1551_WGS
Trace/Mycoplasma_Alligatoris_WGS
Trace/Mycoplasma_Arthritidis_158l3_1_WGS
Trace/Myxococcus_Xanthus_OTHER
Trace/Neorickettsia_Sennetsu_Str__Miyayama_WGS
Trace/Ornithorhynchus_Anatinus_OTHER
Trace/Oryctolagus_Cuniculus_OTHER
Trace/Oryza_Sativa__indica_Cultivar_group__OTHER
Trace/Oryza_Sativa__japonica_Cultivar_group__OTHER
Trace/Otolemur_Garnettii_OTHER
Trace/Ovis_Aries_OTHER
Trace/Pan_Troglodytes_OTHER
Trace/Pan_Troglodytes_WGS
Trace/Papio_Anubis_OTHER
Trace/Papio_Cynocephalus_OTHER
Trace/Paramecium_Tetraurelia_OTHER
Trace/Phanerochaete_Chrysosporium_WGS
Trace/Phytophthora_Infestans_OTHER
Trace/Phytophthora_Infestans_WGS
Trace/Phytophthora_Ramorum_WGS
Trace/Phytophthora_Sojae_WGS
Trace/Plasmodium_Falciparum_OTHER
Trace/Podospora_Anserina_OTHER
Trace/Polypterus_Bichir_OTHER
Trace/Pongo_Pygmaeus_OTHER
Trace/Populus_Balsamifera_WGS
Trace/Porphyromonas_Gingivalis_W83_WGS
Trace/Pseudomonas_Aeruginosa_OTHER
Trace/Pseudomonas_Aeruginosa_WGS
Trace/Pseudomonas_Putida_Kt2440_WGS
Trace/Pseudomonas_Syringae_Pv__Tomato_Str__Dc3000_WGS
Trace/Rattus_Norvegicus_EST
Trace/Rattus_Norvegicus_OTHER
Trace/Rattus_Norvegicus_WGS
Trace/Rhizopus_Oryzae_WGS
Trace/Saccharomyces_Bayanus_WGS
Trace/Saccharomyces_Mikatae_WGS
Trace/Saccharomyces_Paradoxus_WGS
Trace/Saccoglossus_Kowalevskii_WGS
Trace/Saimiri_Boliviensis_Boliviensis_OTHER
Trace/Schistosoma_Mansoni_EST
Trace/Schistosoma_Mansoni_WGS
Trace/Schmidtea_Mediterranea_WGS
Trace/Shewanella_Oneidensis_Mr_1_OTHER
Trace/Silurana_Tropicalis_EST
Trace/Silurana_Tropicalis_OTHER
Trace/Silurana_Tropicalis_WGS
Trace/Sminthopsis_Macroura_OTHER
Trace/Staphylococcus_Aureus_Subsp__Aureus_Col_OTHER
Trace/Staphylococcus_Aureus_Subsp__Aureus_Col_WGS
Trace/Staphylococcus_Epidermidis_Rp62a_OTHER
Trace/Streptococcus_Agalactiae_2603v_r_WGS
Trace/Streptococcus_Pneumoniae_Tigr4_WGS
Trace/Streptococcus_Pyogenes_M1_Gas_OTHER
Trace/Strongylocentrotus_Purpuratus_OTHER
Trace/Strongylocentrotus_Purpuratus_WGS
Trace/Sus_Scrofa_OTHER
Trace/Takifugu_Rubripes_OTHER
Trace/Takifugu_Rubripes_WGS
Trace/Tetrahymena_Thermophila_OTHER
Trace/Tetraodon_Nigroviridis_OTHER
Trace/Tetraodon_Nigroviridis_WGS
Trace/Thalassiosira_Pseudonana_WGS
Trace/Treponema_Denticola_Atcc_35405_WGS
Trace/Triphysaria_Versicolor_EST
Trace/Trypanosoma_Brucei_OTHER
Trace/Ustilago_Hordei_OTHER
Trace/Ustilago_Maydis_WGS
Trace/Vibrio_Cholerae_O1_Biovar_Eltor_Str__N16961_WGS
Trace/Wolbachia_Endosymbiont_Of_Drosophila_Melanogaster_OTHER
Trace/Xenopus_Laevis_EST
Trace/Zea_Mays_EST
Trace/Zea_Mays_OTHER
Trace/Zea_Mays_WGS
+-------------------------------------------------------------+------------+
* The content of each dataset is self-explanatory since they are named using
"/Trace/organism_name_DataType" convention, where the DataType can be EST,
OTHERS, or WGS.
K. Technical Support
Questions and comments on this document and blast in general should be
addressed to:
blast-help@ncbi.nlm.nih.gov
Quesiton and comments on NCBI resources other than BLAST, should be
addressed to:
info@ncbi.nlm.nih.gov