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kblast |
Function
Search similar sequences in public repositories using BLASTDescription
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:
NCBI: http://blast.ncbi.nlm.nih.gov/Blast.cgi
EBI : http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_rest
DDBJ: http://www.xml.nig.ac.jp/wabi/Method?serviceName=DDBJ&mode=methodList&lang=en
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://soap.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]:
Jobid: kbws_1267966
*****
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) | 2 |
| [-outfile] (Parameter 3) |
outfile | Output file name | Output file | <*>.kblast |
| Additional (Optional) qualifiers | ||||
| -d (Parameter 2) |
string | database name about target for your search | Any string | |
| -p | string | blast program name. 'auto' (infer suitable program from your sequence), 'blastn', 'blastp' or 'blastx' | 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 |
| -op | integer | cost to open a gap | Any integer value | -1 |
| -ep | integer | cost to extend a gap | Any integer value | -1 |
| -dropoff | string | X dropoff value for gapped alignment (in bits) | Any string | 0 |
| -q | integer | penalty for a nucleotide mismatch (blastn only) | Any integer value | -3 |
| -r | integer | reward for a nucleotide match (blastn only) | Any integer value | 1 |
| -v | integer | number of database sequences to show one-line descriptions for (V) | Any integer value | 500 |
| -b | 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 |
| -z | 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 |
| -y | 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 optino 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 JapanHistory
2010 - Written by Kazuki OshitaSep 2010 - Added "-format 20" option
Nov 2010 - Revised "-format" option
Target users
This program is intended to be used by everyone and everything, from naive users to embedded scripts.Comments
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 |