バクテリアゲノム解析

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5 GCCGTAGCTACCTTTACAATA GCCGTAGCT AGCTACC GCTACCTTT CCTTTAC CTTTACAATA GCCG CCGT CGTA GTAG TAGC AGCT AGCT GCTA CTAC TACC GCTA CTAC TACC ACCT CCTT CTTT CCTT CTTT TTTA TTAC CTTT TTTA TTAC TACA ACAA CAAT AATA GCCG CTTT TTTA CCGT CCTT TTAC CGTA ACCT TACA GTAG TACC ACAA TAGC CTAC CAAT GCCGTAGCTAC TACCTTTAC AGCT GCTA AATA TACAATA

9 mkdir aaa cd aaa wget ftp://ftp.ddbj.nig.ac.jp//ddbj_database/dra/fastq/sra117/sra117449/srx /SRR _1.fastq.bz2 wget ftp://ftp.ddbj.nig.ac.jp//ddbj_database/dra/fastq/sra117/sra117449/srx /SRR _2.fastq.bz2 bzcat SRR _1.fastq.bz2 head > SRR _1.1M.fastq bzcat SRR _2.fastq.bz2 head > SRR _2.1M.fastq

11 wget -O platanus chmod a+x platanus./platanus Platanus version: /platanus Usage: platanus Command [options] Command: assemble, scaffold, gap_close

12 wget ad07b7376ede/2afddc0e11c6d81e/res/346d91e8-76d9-4f1a c2b0a93f0ab5/run_platanus.sh qsub run_platanus.sh #$ -S /bin/bash #$ -pe def_slot 4 #$ -cwd #$ -l mem_req=4g,s_vmem=4g #$ -l short READ1=SRR _1.1M.fastq READ2=SRR _2.1M.fastq FILE_PREFIX=SRR /platanus assemble -t 4 -m 16 -o ${FILE_PREFIX} -f $READ1 $READ2./platanus scaffold -t 4 -o ${FILE_PREFIX} -c ${FILE_PREFIX}_contig.fa -b ${FILE_PREFIX}_contigBubble.fa -IP1 $READ1 $READ2./platanus gap_close -t 4 -o ${FILE_PREFIX} -c ${FILE_PREFIX}_scaffold.fa -IP1 $READ1 $READ2

13 wget ad07b7376ede/2afddc0e11c6d81e/res/f986e7fa-e95f c cee46/fastalengthfilter.py python fastalengthfilter.py SRR _gapClosed.fa 200 > SRR _200.fa wget ad07b7376ede/2afddc0e11c6d81e/res/8f2b14b b9e a4d07ed62/fasta_stat.py python fasta_stat.py SRR _200.fa TOTAL SEQUENCE LENGTH bp: TOTAL SEQUENCE NUMBER #: 13 LENGTH of 10 LONGEST SEQUENCES: [574295, , , , , 63258, 1415, 1114, 1019, 630] N50: N ratio: %

15 >Chromosome TGGTAATATTACTGTTGATTCATCAACGAGTAGCCCCATAGGGGCAATGGCAAAAGCATACTCCCGTTAATTCGGATGT ATAAATATTAAGTCGAATAAAAGGTATCTAGGAAAACTTGTGAGTACACGTGAAAAACGTCTGCTCTCCTTGCTCTTTT TAAATGAAAAAGAGCCAAAGTCCATAAGGAGGTGTAACAGTTAATGGAACCAAAACGTTATGAAATTACGTACATCATT CGTCCTGACATGGATGAAGCTGCTAAAACAGCGCTTGTTGAACGATTTGACAAGATTGTGTCAGATAATGGTGCTACGA TCGTTGATTCGAAAGACTGGTCTACTCGTCGATTTGCTTATGAAATTGGTGATTACAACGAAGGTACTTACCATATCGT TAATATCACAGCAAACGATGATGTAGCGCTAAACGAATTTGATCGTTTAGCTAAGTTTAGTGACGATATCTTGCGTCAC ATGATTGTTAAGCGTGAAGCTTAATCTAATCAATTTAAAGTTAAGAAAGGAGTATTAGAATCAAACGTGCTCGGATTAT GGGTCTGCTACCATTCGTTGCAGAAGACTAATTTGAAATTGTCCATATTGTATCTCTCGAGCCAATTAAATCAATTAGG AAACTGCCAGAGGAGGGAAATTCAATGGCTCAACAAAGAAGAGGCGGACATCGTCGCCGTAAGGTTGACTTTATTGCCG TTCACAGATTTAAGACACATACTTTTTGTTTTGTGTTCTTGTTTTATTAGTGCTATCGTGTTATAATTTTTGCTTACCG Gene YYY with ZZZ domain Similar to xxx of yyy (zz.z%) Gene XXX Function for xxxxxx AAAAACACGTTCACATCACATAGGCGTTAAAATAATACATCGATTACAAAGATACTGATTTACTAAAACGTTTTATTTC TGAACGCGGTAAGATTTTACCACGTCGATTTAATGTAAATGTTTATTTAAATCCTAATTATGCCATGATTGTGGTGTGA TTAGGTCTCGTCCCGTAAGGTAAGAACATTAACAATATCACCCACTATATGATTAATCGTACAATTCTTGTTGGACGCT TAACTAGAGATCCTGAGTTGCGATACACAACTAGTGGAGCTGCTGTAGCAACGTTTACCGTTGCTGTCAATCGGCAGTT TACCAATCAACAGGGTGAACGGGAAGCTGATTTTATTAGCTGCGTCATTTGGCGTAAAGCTGCTGAAAATTTTTCCAAT TTCACTCATAAGGGTTCTTTGGTTGGGGTTGATGGCCGCATTCAAACGCGAAATTATGAAAATCAACAGGGTCAACGTG TTTATGTAACGGAAGTAGTAGTTGAAAACTTCTCGTTACTAGAAACGAAAGCCCAAAGTCAAAACCATAATAATGGTGC CCCAAGCTTTGACAATAATCAACAAGCCAATGCTCCTCAATCATCATCAGCAAATGATAATCCGTTTGGTAATGCTAAT GACAATGCAAATGCGGGAAGTAGTAGTGCTAACAGCAATGCTAACGATCCATTCGCTAATAATGGCGAACCAATCGACA TTTCAGATGACGATTTGCCGTTCTAACAAAGTTAGTGGAACAAGTGCTAAAAACCAGCGTCGTTTAACAATTGCAATCA AACGTGCTCGGATTATGGGTCTGCTACCATTCGTTGCAGAAGACTAATTTGAAATTGTTTTAAT...

16 Data submission Prerequisite for paper Sequence data Public sequence databases Genome annotation / data submission pipelines PGAP 1~2 weeks to get results Limited for GenBank submitters GenBank Intensive manual curation

17 DDBJ Fast Annotation and Submission Tool Prokaryotic genome annotation Data submission to DDBJ Fast, flexible, and powerful

18 Graphical user interface for beginners Command operations for experts (DFAST-core) Create DDBJ submission file using online editor Sample usage dfast --genome your_genome.fna --config sample.cfg Stand-alone version available for download (

19 assembly gap Genomic FASTA file CDS rrna trna Structural annotation phase de facto standard gene prediction tools parallel processing Collect features Resolve overlap Functional Annotation Functional annotation phase Ultrafast homology search using GHOSTX - 10 times faster Small, but well-curated references (Suzuki et al. 2014) - Default database constructed from 120 representative genomes - Optional organism-specific database Output (GenBank, GFF, DDBJ-MSS...) Pseudogene detection Flexible and customizable

21 wget tar xvfz tar.gz cd dfast_core-1.0.5/ python3 dfast -h python3 scripts/file_downloader.py --protein dfast python3 dfast --config example/test_config.py

22 cd.. export _JAVA_OPTIONS="-Xmx256m -XX:ParallelGCThreads=1" python3 dfast_core-1.0.5/dfast --genome SRR _200.fa --out result -- no_cdd --no_hmm

AJACS18_ ppt

AJACS18_ ppt 1, 1, 1, 1, 1, 1,2, 1,2, 1 1 DDBJ 2 AJACS3 2010 6 414:20-15:20 2231 DDBJ DDBJ DDBJ DDBJ NCBI (GenBank) DDBJ EBI (EMBL-Bank) GEO DDBJ Omics ARchive(DOR) ArrayExpress DTA (DDBJ Trace Archive) DRA (DDBJ