Trad DDBJ. DNA Data Bank of Japan
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2 Trad DDBJ DNA Data Bank of Japan
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5 LOCUS HUMIL2HOM 397 bp DNA linear HUM 27-APR-1993 DEFINITION Human interleukin 2 (IL-2)-like DNA. ACCESSION M13784 VERSION M KEYWORDS. SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 397) AUTHORS Mita,S., Maeda,S. and Shimada,K. TITLE Characterization of human genomic DNA sequences homologous to the interleukin 2 cdna JOURNAL Biochem. Biophys. Res. Commun. 138 (2), (1986) PUBMED COMMENT Original source text: Human placenta DNA, clone Lm HoIL2-3. Numerous stop codons are found in the interleukin 2-like IIa DNA. FEATURES Location/Qualifiers source /organism="homo sapiens" /mol_type="genomic DNA" /db_xref="taxon:9606" BASE COUNT 117 a 84 c 48 g 148 t ORIGIN RsaI site. 1 actgatttat ttttaataaa attacaagag attttaattt taaacccaaa agttctttta 61 ttgcatctca ctgtgtttag ctttgtttac cctttgagaa ggcctgagat aataactttc 121 ttcttcaact ctttcatcag ctcctgtaac cttttttcct taggttctta actgatgttg 181 tggcctgctg ctaaaaacgc tttatcttaa agttctaaaa ggaaatgttt tcttctaaca 241 taacattctg ggctcttgac tttatgaaat caaaaacttt cacttatgac caggatacac 301 tcttcctctg tctaactaat tcaagcacta tcttcattca ttttgacttg cagattatcc 361 aaacagactc cccataatga aaagcaatca cactgca //
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7 Images created by the Wordle.net web application are licensed under a Creative Commons Attribution 3.0 United States License.
8 New DB s and Services for NGS
9 NGS Next-Generation Sequencer New Generation Sequencer
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14 MinION - $900 usb-powered DNA sequencer
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18 Oh! Year! (me) Not nessessary to use SRA site. DDBJ DRA is fast to download! Easy to understand! DRAsearch is extremely handy!
19 200" 175" 150" 125" DRA (DDBJ) ERA (EBI) SRA (NCBI) 100" 75" 50" 25" 0" 2008(01_03" 2008(04_06" 2008(07_09" 2009(10_12" 2009(01_03" 2009(04_06" 2009(07_09" 2010(10_12" 2010(01_03" 2010(04_06" 2010(07_09" 2011(10_12" 2011(01_03" 2011(04_06" 2011(10_12"
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27 MinION - $900 usb-powered DNA sequencer
28 good references good pipelines
29 good references good pipelines
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31 >gi emb CAJ strongly imilar to aspartate aminotransferase [Candidatus Kuenenia stuttgartiensis] MIASRMSNIDSSGIRKVFDLAQKMKSPVNLSIGQPDFDVPGEIKEVAIKSINEGANKYTLTQGIPELRNV... >gi gb AAP predicted methyl transferas [Mycoplasma gallisepticum R] MSALYLVGLPIGNLSEINHRALEILNQLEIIYCENTDNFKKLLNLLNINFRDKKLISYHKFNETNRFIMI... similar to transferase
32 LOCUS XM_ bp mrna linear INV 12-APR-2011 DEFINITION PREDICTED: Apis mellifera septin-2 (2-Sep), mrna. ACCESSION XM_ VERSION XM_ GI: KEYWORDS. SOURCE Apis mellifera (honey bee) ORGANISM Apis mellifera Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Apidae; Apis. COMMENT MODEL REFSEQ: This record is predicted by automated computational analysis. This record is derived from a genomic sequence (NW_ ) annotated using gene prediction method: GNOMON, supported by EST evidence. Also see: Documentation of NCBI's Annotation Process On Apr 12, 2011 this sequence version replaced gi: FEATURES Location/Qualifiers source /organism="apis mellifera" /mol_type="mrna" /strain="dh4" /db_xref="taxon:7460" /linkage_group="lg6" gene /gene="2-sep" /note="derived by automated computational analysis using gene prediction method: GNOMON. Supporting evidence includes similarity to: 436 ESTs, 11 Proteins" /db_xref="beebase:gb17411" /db_xref="geneid:408882" misc_feature /gene="2-sep" /note="upstream in-frame stop codon" CDS /gene="2-sep" /codon_start=1 /product="septin-2" /protein_id="xp_ "
33 BMC Bioinformatics 2004, 5:80 doi: /
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48 good references good pipelines
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50 Special machines for big memory (de novo assembly)
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53 # run a script on a thin node. qsub cwd S /bin/bash your_script.sh # run a script on a medium node. qsub cwd l month l medium S /bin/bash your_script.sh # run a script on the fat node. qsub cwd l month l fat S /bin/bash your_script.sh
54 # This job runs on 1 CPU core and 128GB memory. qsub cwd l month -l medium -l s_vmem=128g,mem_req=128g S /bin/bash your_script.sh # This job runs on 10 CPU core (in the same node) and 1280GB memory. qsub cwd l month -l medium -l s_vmem=128g,mem_req=128g -pe def_slot=10 S /bin/bash your_script.sh
55 It s easy to use, isn t it? ( )
56 ( д )...What? ( )
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58 :Cloud_computing_icon.svg CC-BY-SA 3.0 by
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60 de facto standard tools
61 major genome sets in several versions
62 DNA DropBox of Japan
63 @SRR :7:1:830:763 length=36 GTCAATATTAATCATACCAATATACTCAAAAAATAA +SRR :7:1:830:763 length= :7:1:402:781 length=36 GGTCTAAAAAGCAAAATTCAGTCTTCAAAATAATTC +SRR :7:1:402:781 length= :7:1:433:775 length=36 GTGCTTTTTTTTTTCCAGGAAGTTGTCTCCTCTATC +SRR :7:1:433:775 length=36 II3DI>IIIIIIIB7.,&%&'&)."+%,$"&$&"%# low-data assemble mapping Report! BLAST gene-finding...
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Yutaka Ueno Neuroscience, AIST Tsukuba, Japan
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