kblast

Function

Search similar sequences in public repositories using BLAST

Description

kblast finds regions of local similarity between sequences used BLAST (Basic Local Alignment Search Tool). kblast is supported "blastn", "blastp" and "blastx" methods. BLAST compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

kblast utilizing three BLAST web services produced by NCBI(National Center for Biotechnology Information), EBI (European Bioinformatics Institute) and DDBJ (DNA Data Bank of Japan). original web-services is located at the following URL:

kblast is able to search against all databases produced by those service providers. This program selects automatically and accesses a provider which supports the database you specified. Available databases are listed in the Notes section.

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kblast is an interface of "runBlast" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://www.g-language.org/kbws/ for more information.

Usage


  Here is a sample session with kblast

% kblast
Search similar sequences in public repositories using BLAST
Input (gapped) sequence(s): swissprot:FOXP2_HUMAN
database name about target for your search: swissprot
Output file [foxp2_human.kblast]: 


BLASTP 2.2.22+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.


RID: STANM4WF01S


Database: Non-redundant SwissProt sequences
432,088 sequences; 159,864,915 total letters
Query=  FOXP2_HUMAN 
Length=715


Score     E
Sequences producing significant alignments:                       (Bits)  Value

sp|Q8MJ98.3|FOXP2_PONPY  RecName: Full=Forkhead box protein P2      776    0.0   
sp|Q5QL03.1|FOXP2_HYLLA  RecName: Full=Forkhead box protein P2      776    0.0   
sp|Q8MJ99.1|FOXP2_GORGO  RecName: Full=Forkhead box protein P2      776    0.0   
sp|Q8MJA0.1|FOXP2_PANTR  RecName: Full=Forkhead box protein P2...   776    0.0   
sp|P58463.2|FOXP2_MOUSE  RecName: Full=Forkhead box protein P2      776    0.0   
sp|Q8MJ97.1|FOXP2_MACMU  RecName: Full=Forkhead box protein P2      776    0.0   
sp|O15409.2|FOXP2_HUMAN  RecName: Full=Forkhead box protein P2...   776    0.0   
sp|Q4VYS1.1|FOXP2_XENLA  RecName: Full=Forkhead box protein P2...   754    0.0   
sp|Q5W1J5.1|FOXP1_XENLA  RecName: Full=Forkhead box protein P1...   524    7e-148
sp|A4IFD2.1|FOXP1_BOVIN  RecName: Full=Forkhead box protein P1      518    4e-146
sp|Q9H334.1|FOXP1_HUMAN  RecName: Full=Forkhead box protein P1      513    2e-144
sp|Q498D1.1|FOXP1_RAT  RecName: Full=Forkhead box protein P1        511    8e-144
sp|P58462.1|FOXP1_MOUSE  RecName: Full=Forkhead box protein P1...   510    1e-143
sp|Q58NQ4.1|FOXP1_CHICK  RecName: Full=Forkhead box protein P1      510    1e-143
sp|Q2LE08.1|FXP1B_DANRE  RecName: Full=Forkhead box protein P1-B    484    1e-135
sp|Q8IVH2.1|FOXP4_HUMAN  RecName: Full=Forkhead box protein P4...   468    6e-131
sp|Q9DBY0.1|FOXP4_MOUSE  RecName: Full=Forkhead box protein P4...   453    2e-126
sp|Q4VYR7.1|FOXP4_XENLA  RecName: Full=Forkhead box protein P4...   451    6e-126
sp|Q99JB6.1|FOXP3_MOUSE  RecName: Full=Forkhead box protein P3...   215    1e-54 
sp|Q6U8D7.1|FOXP3_MACFA  RecName: Full=Forkhead box protein P3      209    7e-53 
sp|Q9BZS1.1|FOXP3_HUMAN  RecName: Full=Forkhead box protein P3...   209    7e-53 
sp|Q66IG8.1|FXJ12_XENTR  RecName: Full=Forkhead box protein J1...  90.5    4e-17 
sp|Q32NH9.1|FXJ12_XENLA  RecName: Full=Forkhead box protein J1...  89.7    6e-17 
sp|Q5M7N6.2|FOXJ1_XENTR  RecName: Full=Forkhead box protein J1...  87.0    4e-16 
sp|Q708W1.1|FXJ1B_XENLA  RecName: Full=Forkhead box protein J1...  87.0    4e-16 

( omitting... )

ALIGNMENTS
>sp|Q8MJ98.3|FOXP2_PONPY RecName: Full=Forkhead box protein P2
Length=713

Score =  776 bits (2005),  Expect = 0.0
Identities = 456/458 (99%), Positives = 457/458 (99%), Gaps = 0/458 (0%)

Query  240  GLISIPPGQAALPVQSLPQAGLSPAEIQQLWKEVTGVHSMEDNGIKHGGLDLttnnssst  299
GLISIPPGQAALPVQSLPQAGLSPAEIQQLWKEVTGVHSMEDNGIKHGGLDLTTNNSSST
Sbjct  238  GLISIPPGQAALPVQSLPQAGLSPAEIQQLWKEVTGVHSMEDNGIKHGGLDLTTNNSSST  297

Query  300  tssntsKASPPITHHSIVNGQssvlsarrdsssHEETGASHTLYGHGVCKWPGCESICED  359
TSS TSKASPPITHHSIVNGQSSVL+ARRDSSSHEETGASHTLYGHGVCKWPGCESICED
Sbjct  298  TSSTTSKASPPITHHSIVNGQSSVLNARRDSSSHEETGASHTLYGHGVCKWPGCESICED  357

Query  360  FGQFLKHLNNEHALDDRSTAQCRVQMQVVQQLEIQLSKERERLQAMMTHLHMRPSEPKPS  419
FGQFLKHLNNEHALDDRSTAQCRVQMQVVQQLEIQLSKERERLQAMMTHLHMRPSEPKPS
Sbjct  358  FGQFLKHLNNEHALDDRSTAQCRVQMQVVQQLEIQLSKERERLQAMMTHLHMRPSEPKPS  417

Query  420  PKPLNLVSSVTMSKNMLEtspqslpqtpttptapvtpitqGPSVITPASVPNVGAIRRRH  479
PKPLNLVSSVTMSKNMLETSPQSLPQTPTTPTAPVTPITQGPSVITPASVPNVGAIRRRH
Sbjct  418  PKPLNLVSSVTMSKNMLETSPQSLPQTPTTPTAPVTPITQGPSVITPASVPNVGAIRRRH  477

Query  480  SDKYNIPMSSEIAPNYEFYKNADVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFA  539
SDKYNIPMSSEIAPNYEFYKNADVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFA
Sbjct  478  SDKYNIPMSSEIAPNYEFYKNADVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFA  537

Query  540  YFRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEVEYQKRRSQKITGSPTLVKNIP  599
YFRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEVEYQKRRSQKITGSPTLVKNIP
Sbjct  538  YFRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEVEYQKRRSQKITGSPTLVKNIP  597

Query  600  TSLGYGaalnaslqaalaesslpllsNPGLINNASSGLLQAVHEDLNGSLDHIDSNGNSS  659
TSLGYGAALNASLQAALAESSLPLLSNPGLINNASSGLLQAVHEDLNGSLDHIDSNGNSS
Sbjct  598  TSLGYGAALNASLQAALAESSLPLLSNPGLINNASSGLLQAVHEDLNGSLDHIDSNGNSS  657

Query  660  PGCSPQPHIHSIHVKEEPVIAEDEDCPMSLVTTANHSP  697
PGCSPQPHIHSIHVKEEPVIAEDEDCPMSLVTTANHSP
Sbjct  658  PGCSPQPHIHSIHVKEEPVIAEDEDCPMSLVTTANHSP  695


Score =  112 bits (279),  Expect = 1e-23
Identities = 99/100 (99%), Positives = 99/100 (99%), Gaps = 0/100 (0%)

Query  1   MMQESATETISNSSMNQNGMSTLSSQLDAgsrdgrssgdtssEVSTVEllhlqqqqalqa  60
MMQES TETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
Sbjct  1   MMQESVTETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA  60

Query  61  arqlllqqqTSGLKSPKSSDKQRPLQVPVSVAMMTPQVIT  100
ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVIT
Sbjct  61  ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVIT  100


>sp|Q5QL03.1|FOXP2_HYLLA RecName: Full=Forkhead box protein P2
Length=713

Score =  776 bits (2005),  Expect = 0.0
Identities = 456/458 (99%), Positives = 457/458 (99%), Gaps = 0/458 (0%)

Query  240  GLISIPPGQAALPVQSLPQAGLSPAEIQQLWKEVTGVHSMEDNGIKHGGLDLttnnssst  299
GLISIPPGQAALPVQSLPQAGLSPAEIQQLWKEVTGVHSMEDNGIKHGGLDLTTNNSSST
Sbjct  238  GLISIPPGQAALPVQSLPQAGLSPAEIQQLWKEVTGVHSMEDNGIKHGGLDLTTNNSSST  297

Query  300  tssntsKASPPITHHSIVNGQssvlsarrdsssHEETGASHTLYGHGVCKWPGCESICED  359
TSS TSKASPPITHHSIVNGQSSVL+ARRDSSSHEETGASHTLYGHGVCKWPGCESICED
Sbjct  298  TSSTTSKASPPITHHSIVNGQSSVLNARRDSSSHEETGASHTLYGHGVCKWPGCESICED  357

Query  360  FGQFLKHLNNEHALDDRSTAQCRVQMQVVQQLEIQLSKERERLQAMMTHLHMRPSEPKPS  419
FGQFLKHLNNEHALDDRSTAQCRVQMQVVQQLEIQLSKERERLQAMMTHLHMRPSEPKPS
Sbjct  358  FGQFLKHLNNEHALDDRSTAQCRVQMQVVQQLEIQLSKERERLQAMMTHLHMRPSEPKPS  417

Query  420  PKPLNLVSSVTMSKNMLEtspqslpqtpttptapvtpitqGPSVITPASVPNVGAIRRRH  479
PKPLNLVSSVTMSKNMLETSPQSLPQTPTTPTAPVTPITQGPSVITPASVPNVGAIRRRH
Sbjct  418  PKPLNLVSSVTMSKNMLETSPQSLPQTPTTPTAPVTPITQGPSVITPASVPNVGAIRRRH  477

Query  480  SDKYNIPMSSEIAPNYEFYKNADVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFA  539
SDKYNIPMSSEIAPNYEFYKNADVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFA
Sbjct  478  SDKYNIPMSSEIAPNYEFYKNADVRPPFTYATLIRQAIMESSDRQLTLNEIYSWFTRTFA  537

Query  540  YFRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEVEYQKRRSQKITGSPTLVKNIP  599
YFRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEVEYQKRRSQKITGSPTLVKNIP
Sbjct  538  YFRRNAATWKNAVRHNLSLHKCFVRVENVKGAVWTVDEVEYQKRRSQKITGSPTLVKNIP  597

Query  600  TSLGYGaalnaslqaalaesslpllsNPGLINNASSGLLQAVHEDLNGSLDHIDSNGNSS  659
TSLGYGAALNASLQAALAESSLPLLSNPGLINNASSGLLQAVHEDLNGSLDHIDSNGNSS
Sbjct  598  TSLGYGAALNASLQAALAESSLPLLSNPGLINNASSGLLQAVHEDLNGSLDHIDSNGNSS  657

Query  660  PGCSPQPHIHSIHVKEEPVIAEDEDCPMSLVTTANHSP  697
PGCSPQPHIHSIHVKEEPVIAEDEDCPMSLVTTANHSP
Sbjct  658  PGCSPQPHIHSIHVKEEPVIAEDEDCPMSLVTTANHSP  695


Score =  113 bits (283),  Expect = 4e-24
Identities = 100/100 (100%), Positives = 100/100 (100%), Gaps = 0/100 (0%)

Query  1   MMQESATETISNSSMNQNGMSTLSSQLDAgsrdgrssgdtssEVSTVEllhlqqqqalqa  60
MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA
Sbjct  1   MMQESATETISNSSMNQNGMSTLSSQLDAGSRDGRSSGDTSSEVSTVELLHLQQQQALQA  60

Query  61  arqlllqqqTSGLKSPKSSDKQRPLQVPVSVAMMTPQVIT  100
ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVIT
Sbjct  61  ARQLLLQQQTSGLKSPKSSDKQRPLQVPVSVAMMTPQVIT  100

( omitting... )


Database: Non-redundant SwissProt sequences
Posted date:  Feb 28, 2010  5:41 PM
Number of letters in database: 159,864,915
Number of sequences in database:  432,088

Lambda     K      H
0.313    0.128    0.376 
Gapped
Lambda     K      H
0.267   0.0410    0.140 
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 432088
Number of Hits to DB: 7717384
Number of extensions: 257555
Number of successful extensions: 471
Number of sequences better than 10: 3
Number of HSP's better than 10 without gapping: 0
Number of HSP's gapped: 473
Number of HSP's successfully gapped: 4
Length of query: 715
Length of database: 159864915
Length adjustment: 124
Effective length of query: 591
Effective length of database: 106286003
Effective search space: 62815027773
Effective search space used: 62815027773
T: 11
A: 40
X1: 16 (7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (20.8 bits)
S2: 73 (32.7 bits)

	    

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)
seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) Required
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kblast
Additional (Optional) qualifiers
-database
string database name about target for your search Any string swissprot
-program string blast program name. 'auto' (infer suitable program from your sequence), 'blastn', 'blastp' or 'blastx'. 'auto' selects an appropriate program automatically judged from your sequence and database. Any string auto
-server string specify web server for your search. 'NCBI', 'EBI' or 'DDBJ' Any string
-format integer blast report format
0 : normal BLAST report
8 : tabular
k1: ID list
k2: ID list separated by conmma
Any string 0
-eval string Expectation value Any numeric value 10.0
-qfilter string [T/F] filter query sequence Any string T
-opengap integer cost to open a gap Any integer value -1
-extendgap integer cost to extend a gap Any integer value -1
-dropoff string X dropoff value for gapped alignment (in bits) Any string 0
-penalty integer penalty for a nucleotide mismatch (blastn only) Any integer value -3
-reward integer reward for a nucleotide match (blastn only) Any integer value 1
-numdescriptions integer number of database sequences to show one-line descriptions for (V) Any integer value 500
--numalignments integer number of database sequence to show alignments for (B) Any integer value 250
-threshold integer threshold for extending hits, default if zero for each program Any integer value 0
-g boolean perform gapped alignment Boolean value Yes/No No
-matrix string matrix Any string BLOSUM62
-wordsize integer word size, default if zero for each program Any integer value 0
-dbsize float effective length of the database Any numeric value 0
-k integer number of best hits from a region to keep Any integer value 0
-searchsp float effective length of the search space Any numeric value 0
Advanced (Unprompted) qualifiers
(none)

Input file format

kblast can use any genome sequence data that seqret can read.

Output file format

The output from kblast is general BLAST report format. Moreover kblast is able to use -m8 option.

Data files

None.

Notes

None.

References

	Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic 
        local alignment search tool, J Mol Biol, 215, 403-410.

	Altschul S.F., et al.,(1997) Gapped BLAST and PSI-BLAST: a new generation
	of protein database search programs, Nucleic Acids Research, 25(17), 3389-3402.

	McWilliam H., et al.,(2009) Web services at the European Bioinformatics Institute
	Nucleic Acids Research Web Server Issue 2009, 37, W6-W10.
      

Warnings

Because of problem in system, we cannot help setting some different option names from original BLAST.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
kshowblastdb Displays information on databases for kblast
kssearch Search similar sequences in public repositories using SSEARCH
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org)
Institute for Advanced Biosciences, Keio University
252-8520 Japan

History

2010 - Written by Kazuki Oshita
Sep 2010 - Added "-format 20" option
Nov 2010 - Revised "-format" option
Mar 2013 - Changed options' name and update document by Kazuki Oshita

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None.

Appendix

The list of available databases is below.

blastp

Server Name Short explanation
DDBJ DAD DAD data
PDB PDB data
PDBSH PDBSH data
PRF PRF data
PROTEIN PROTEIN data
SWISS SWISSPROT data
WORMPEP WORM PEPTIDE data
UNIPROT UNIPROT data
TREMBL TREMBL data
EBI uniprot UniProt
swissprot UniProtKB/Swiss-Prot
uniref100 UniRef 100
uniref90 UniRef 90
uniref50 UniRef 50
uniparc UniParc
ipi International
pdb Protein
sgt Structural
intact IntAct
imgthlap IMGT/HLA
epop EPO
jpop JPO
kpop KIPO
uspop USPTO
NCBI nr nr, protein
refseq_protein refseq protein
swissprot swissprot protein
pataa pat protein
pdbaa pdb protein
month.pataa month pat protein
monthaa month protein
alu alu repeat protein
env_nr env protein

blastn

Server Name Short explanation
DDBJ DDBJ DDBJ Release and New data includes all division
DDBJ_EXEST DDBJ Release and New data except EST division
DDBJNEW DDBJ New data includes all division
DDBJNEW_EXEST DDBJ New data except EST division
ddbjbct DDBJ Bacteria division
ddbjenv DDBJ Env division
ddbjest DDBJ EST division
ddbjgss DDBJ Genome Survey Sequences division
ddbjhtg DDBJ High Throughput Genomic sequencing division
ddbjhum DDBJ human division
ddbjinv DDBJ invertebrates division
ddbjmam DDBJ other mammals division
ddbjpat DDBJ patens division
ddbjphg DDBJ phages division
ddbjpln DDBJ plants, fugi and algae division
ddbjpri DDBJ primates division
ddbjrna DDBJ rna (structual RNAs) division
ddbjrod DDBJ rodents division
ddbjsts DDBJ sts division
ddbjsyn DDBJ synthetic sequences division
ddbjtsa DDBJ TSA(Transcriptome Shotgun Assembly) division
ddbjuna DDBJ unannotated sequences division
ddbjvrl DDBJ viruses division
ddbjvrt DDBJ other vertebrates division
est_atha A.thaliana
est_btra B.taurus
est_cele C.elegans
est_cint C.intestinalis
est_crei C.reinhardtii
est_ddis D.discoideum
est_dmel D.melanogaster
est_drer D.rerio
est_ggal G.gallus
est_gmax G.max
est_hum H.sapiens
est_hvul H.vulgare
est_mous M.musculus
est_mtru M.truncatula
est_osat O.sativa
est_rnor R.norvegicus
est_slyc S.lycopersicum
est_taes T.aestivum
est_xlae X.laevis
est_xtro X.tropicalis
est_zmay Z.mays
est_rest Others
EBI em_rel EMBL Release
emnew EMBL Updates
emcds EMBL Coding Sequence
em_rel_env All EMBL Environmental
em_rel_est_env EMBL EST Environmental
em_rel_gss_env EMBL GSS Environmental
em_rel_htc_env EMBL HTC Environmental
em_rel_htg_env EMBL HTG Environmental
em_rel_pat_env EMBL Patent Environmental
em_rel_std_env EMBL Standard Environmental
em_rel_fun All EMBL Fungi
em_rel_est_fun EMBL EST Fungi
em_rel_gss_fun EMBL GSS Fungi
em_rel_htc_fun EMBL HTC Fungi
em_rel_htg_fun EMBL HTG Fungi
em_rel_pat_fun EMBL Patent Fungi
em_rel_std_fun EMBL Standard Fungi
em_rel_sts_fun EMBL STS Fungi
em_rel_tpa_fun EMBL TPA Fungi
em_rel_tsa_fun EMBL TSA Fungi
em_rel_hum All EMBL Human
em_rel_est_hum EMBL EST Human
em_rel_gss_hum EMBL GSS Human
em_rel_htc_hum EMBL HTC Human
em_rel_htg_hum EMBL HTG Human
em_rel_pat_hum EMBL Patent Human
em_rel_std_hum EMBL Standard Human
em_rel_sts_hum EMBL STS Human
em_rel_tpa_hum EMBL TPA Human
em_rel_inv All EMBL Invertebrate
em_rel_est_inv EMBL EST Invertebrate
em_rel_gss_inv EMBL GSS Invertebrate
em_rel_htc_inv EMBL HTC Invertebrate
em_rel_htg_inv EMBL HTG Invertebrate
em_rel_pat_inv EMBL Patent Invertebrate
em_rel_std_inv EMBL Standard Invertebrate
em_rel_sts_inv EMBL STS Invertebrate
em_rel_tpa_inv EMBL TPA Invertebrate
em_rel_tsa_inv EMBL TSA Invertebrate
em_rel_mam All EMBL Mammal
em_rel_est_mam EMBL EST Mammal
em_rel_gss_mam EMBL GSS Mammal
em_rel_htc_mam EMBL HTC Mammal
em_rel_htg_mam EMBL HTG Mammal
em_rel_pat_mam EMBL Patent Mammal
em_rel_std_mam EMBL Standard Mammal
em_rel_sts_mam EMBL STS Mammal
em_rel_tpa_mam EMBL TPA Mammal
em_rel_tpa_mam EMBL TSA Mammal
em_rel_mus All EMBL Mouse
em_rel_est_mus EMBL EST Mouse
em_rel_gss_mus EMBL GSS Mouse
em_rel_htc_mus EMBL HTC Mouse
em_rel_htg_mus EMBL HTG Mouse
em_rel_pat_mus EMBL Patent Mouse
em_rel_std_mus EMBL Standard Mouse
em_rel_sts_mus EMBL STS Mouse
em_rel_tpa_mus EMBL TPA Mouse
em_rel_phg All EMBL Phage
em_rel_gss_phg EMBL GSS Phage
em_rel_htg_phg EMBL HTG Phage
em_rel_pat_phg EMBL Patent Phage
em_rel_std_phg EMBL Standard Phage
em_rel_tpa_phg EMBL TPA Phage
em_rel_pln All EMBL Plant
em_rel_est_pln EMBL EST Plant
em_rel_gss_pln EMBL GSS Plant
em_rel_htc_pln EMBL HTC Plant
em_rel_htg_pln EMBL HTG Plant
em_rel_pat_pln EMBL Patent Plant
em_rel_std_pln EMBL Standard Plant
em_rel_sts_pln EMBL STS Plant
em_rel_tpa_pln EMBL TPA Plant
em_rel_tsa_pln EMBL TSA Plant
em_rel_pro All EMBL Prokaryote
em_rel_est_pro EMBL EST Prokaryote
em_rel_gss_pro EMBL GSS Prokaryote
em_rel_htc_pro EMBL HTC Prokaryote
em_rel_htg_pro EMBL HTG Prokaryote
em_rel_pat_pro EMBL Patent Prokaryote
em_rel_std_pro EMBL Standard Prokaryote
em_rel_sts_pro EMBL STS Prokaryote
em_rel_tpa_pro EMBL TPA Prokaryote
em_rel_rod All EMBL Rodent
em_rel_est_rod EMBL EST Rodent
em_rel_gss_rod EMBL GSS Rodent
em_rel_htc_rod EMBL HTC Rodent
em_rel_htg_rod EMBL HTG Rodent
em_rel_pat_rod EMBL Patent Rodent
em_rel_std_rod EMBL Standard Rodent
em_rel_sts_rod EMBL STS Rodent
em_rel_tpa_rod EMBL TPA Rodent
em_rel_syn All EMBL Synthetic
em_rel_pat_syn EMBL Patent Synthetic
em_rel_std_syn EMBL Standard Synthetic
em_rel_tpa_syn EMBL TPA Synthetic
em_rel_tgn All EMBL Transgenic
em_rel_std_tgn EMBL Standard Transgenic
em_rel_gss_tgn EMBL GSS Transgenic
em_rel_unc All EMBL Unclassified
em_rel_est_unc EMBL EST Unclassified
em_rel_pat_unc EMBL Patent Unclassified
em_rel_std_unc EMBL Standard Unclassified
em_rel_tpa_unc EMBL TPA Unclassified
em_rel_vrl All EMBL Viral
em_rel_gss_vrl EMBL GSS Viral
em_rel_htg_vrl EMBL HTG Viral
em_rel_pat_vrl EMBL Patent Viral
em_rel_std_vrl EMBL Standard Viral
em_rel_tpa_vrl EMBL TPA Viral
em_rel_vrt All EMBL Vertebrate
em_rel_est_vrt EMBL EST Vertebrate
em_rel_gss_vrt EMBL GSS Vertebrate
em_rel_htc_vrt EMBL HTC Vertebrate
em_rel_htg_vrt EMBL HTG Vertebrate
em_rel_pat_vrt EMBL Patent Vertebrate
em_rel_std_vrt EMBL Standard Vertebrate
em_rel_sts_vrt EMBL STS Vertebrate
em_rel_tpa_vrt EMBL TPA Vertebrate
em_rel_tsa_vrt EMBL TSA Vertebrate
em_rel_est EMBL Expressed Sequence Tag
em_rel_gss EMBL Genome Survey Sequence
em_rel_htc EMBL High Throughput cDNA
em_rel_htg EMBL High Throughput Genome
em_rel_pat EMBL Patent
em_rel_std EMBL Standard
em_rel_sts EMBL Sequence Tagged Site
em_rel_tpa EMBL Third Party Annotation
emall EMBL Release and Updates
evec EMBL Vectors
imgtligm IMGT/LIGM-DB
imgthla IMGT/HLA
hgvbase HGVBASE
NCBI 10090_genomic mouse genomic
10116_genomic rat genomic
180454_genomic anopheles gambiae genomic
7070_genomic red flour beetle genomic
7460_genomic honey bee genomic
7955_genomic zebrafish genomic
9031_genomic chicken genomic
9544_genomic macaca genomic
9598_genomic chimp genomic
9606_genomic human genomic
9615_genomic dog genomic
9913_genomic cow genomic
chromosome chromosomes
other_genomic other genomic
refseq_genomic refseq genomic
refseq_rna refseq rna
env_nt env_nt
est est combined
est_human est human
est_mouse est mouse
est_others est others
sts sts
gss gss
htgs htgs
month.est month est
month.gss month gss
month.htgs month htgs
month.nt month nt
month.patnt month patnt
month.sts month sts
monthnt month nt
Test/gpipe/9606/allcontig_and_rna human genomic and transcripts
Test/gpipe/10090/allcontig_and_rna mouse genomic and transcripts
nt nt, nucleotide nr
patnt pat nucleotide
pdbnt pdb nucleotide
wgs wgs
UniVec UniVec vector library
alu alu repeat
danio.lib danio rerio repeats
humrep combined human repeat libraries
rodents.lib rodents repeats
geo geo (geo)
cdsearch/cdd cdd
cdsearch/oasis_cog cog
cdsearch/oasis_kog kog
cdsearch/oasis_pfam pfam
cdsearch/oasis_smart smart
repeat/repeat_3055 Chlamydomonas reinhardtii
repeat/repeat_31032 Fugu
repeat/repeat_35128 Thalassiosira pseudonana
repeat/repeat_3702 Arabidopsis thaliana
repeat/repeat_40674 Mammalia
repeat/repeat_4530 Oryza sativa
repeat/repeat_4751 Fungi
repeat/repeat_6238 Caenorhabditis briggsae
repeat/repeat_6239 Caenorhabditis elegans
repeat/repeat_7165 Anopheles gambiae
repeat/repeat_7227 Drosophila melanogaster
repeat/repeat_7719 Ciona intestinalis
repeat/repeat_7955 Danio rerio
repeat/repeat_9606 Human
repeat/repeat_9989 Rodentia