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